Last updated: 2021-03-22

Checks: 7 0

Knit directory: transcriptome_cll/

This reproducible R Markdown analysis was created with workflowr (version 1.4.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

Seed: set.seed(20190511)

The command set.seed(20190511) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: relative

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Repository version: 50a8daa

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:


Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    output/figures/r_objects/BRAF/enrichment/

Untracked files:
    Untracked:  docs/figure/ATM.Rmd/
    Untracked:  docs/figure/BRAF.Rmd/
    Untracked:  docs/figure/Del13q14.Rmd/
    Untracked:  docs/figure/Del17p13.Rmd/
    Untracked:  docs/figure/Del8p12.Rmd/
    Untracked:  docs/figure/Gain8q24.Rmd/
    Untracked:  docs/figure/IGHV.Rmd/
    Untracked:  docs/figure/Med12.Rmd/
    Untracked:  docs/figure/Notch1.Rmd/
    Untracked:  docs/figure/SF3B1.Rmd/
    Untracked:  docs/figure/TP53.Rmd/
    Untracked:  docs/figure/del11q22.Rmd/
    Untracked:  docs/figure/summary_de_genes.Rmd/
    Untracked:  docs/figure/summary_variants.Rmd/
    Untracked:  output/enrichment/NOTCH1_gsea.rds
    Untracked:  output/enrichment/del13q14_gsea.rds
    Untracked:  output/enrichment/del17p13_gsea.rds
    Untracked:  output/enrichment/gain8q24_gsea.rds
    Untracked:  output/figures/r_objects/BRAF/de_genes/ARNTL2.rds
    Untracked:  output/figures/r_objects/BRAF/de_genes/C9orf139.rds
    Untracked:  output/figures/r_objects/BRAF/de_genes/CD1A.rds
    Untracked:  output/figures/r_objects/BRAF/de_genes/CD1C.rds
    Untracked:  output/figures/r_objects/BRAF/de_genes/CNFN.rds
    Untracked:  output/figures/r_objects/BRAF/de_genes/IGHG1.rds
    Untracked:  output/figures/r_objects/BRAF/de_genes/IGHV3-49.rds
    Untracked:  output/figures/r_objects/BRAF/de_genes/INMT.rds
    Untracked:  output/figures/r_objects/BRAF/de_genes/KIF7.rds
    Untracked:  output/figures/r_objects/BRAF/de_genes/NECAB1.rds
    Untracked:  output/figures/r_objects/BRAF/de_genes/RAB25.rds
    Untracked:  output/figures/r_objects/BRAF/de_genes/SPOCD1.rds
    Untracked:  output/figures/r_objects/BRAF/de_genes/TFCP2L1.rds
    Untracked:  output/figures/r_objects/BRAF/de_genes/TICRR.rds
    Untracked:  output/figures/r_objects/BRAF/de_genes/TMPRSS4.rds
    Untracked:  output/figures/r_objects/Notch1/Notch1_enrichment_dn.rds
    Untracked:  output/figures/r_objects/Notch1/Notch1_enrichment_up.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/AAAS.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/ARHGEF37.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/ASH2LP1.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/CCDC114.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/CD1A.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/CELSR2.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/CNFN.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/CR1.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/DNAH2.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/FOXP2.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/IGHV1-3.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/IGLV1-47.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/IGLV2-23.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/IGLV3-10.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/IGLV4-69.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/IGLV5-37.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/MOB3B.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/OCA2.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/POU6F2.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/SERPINE2.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/SPAG17.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/SPTBN5.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/TMPRSS4.rds
    Untracked:  output/figures/r_objects/atm/de_genes/CYP51A1-AS1.rds
    Untracked:  output/figures/r_objects/atm/de_genes/IGHV1-18.rds
    Untracked:  output/figures/r_objects/atm/de_genes/IGLV3-27.rds
    Untracked:  output/figures/r_objects/atm/de_genes/NCAPGP1.rds
    Untracked:  output/figures/r_objects/atm/de_genes/PPM1E.rds
    Untracked:  output/figures/r_objects/atm/de_genes/PRSS21.rds
    Untracked:  output/figures/r_objects/atm/de_genes/PTPRQ.rds
    Untracked:  output/figures/r_objects/atm/de_genes/SNTB1.rds
    Untracked:  output/figures/r_objects/atm/de_genes/TM6SF1.rds
    Untracked:  output/figures/r_objects/del11q22/de_genes/CLDN3.rds
    Untracked:  output/figures/r_objects/del11q22/de_genes/IGHE.rds
    Untracked:  output/figures/r_objects/del11q22/de_genes/TFCP2L1.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/ARNTL2.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/CCDC151.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/CSGALNACT1.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/FBLN2.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/FRMD5.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/IGHV1-2.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/IGHV3-33.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/IGKV1-39.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/IGKV1-5.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/IGKV1-8.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/IGKV1D-39.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/INHBA.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/LAMP3.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/RAI14.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/RASSF8.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/RNF157.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/SEPT10.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/SLC19A1.rds
    Untracked:  output/figures/r_objects/del13q14/del13q14_enrichment_dn.rds
    Untracked:  output/figures/r_objects/del13q14/del13q14_enrichment_up.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/ARNTL2.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/CDH2.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/CEP55.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/COL6A1.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/FLT4.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/IGHV3-11.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/IGKV1-16.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/KIF7.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/MDM2.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/MEIS1.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/MIR4538.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/MRAP2.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/MYL12BP2.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/NPTX1.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/NRP2.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/PPM1H.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/RNF157.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/SLFNL1.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/SRP72P2.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/TFCP2L1.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/WDR87.rds
    Untracked:  output/figures/r_objects/del17p13/del17p13_enrichment_dn.rds
    Untracked:  output/figures/r_objects/del17p13/del17p13_enrichment_up.rds
    Untracked:  output/figures/r_objects/del8p12/de_genes/IGHJ2P.rds
    Untracked:  output/figures/r_objects/del8p12/de_genes/OVCH1-AS1.rds
    Untracked:  output/figures/r_objects/del8p12/de_genes/PLCB1.rds
    Untracked:  output/figures/r_objects/del8p12/de_genes/TM6SF1.rds
    Untracked:  output/figures/r_objects/epistasis/de_genes/CD38.rds
    Untracked:  output/figures/r_objects/gain8q24/de_genes/C1orf127.rds
    Untracked:  output/figures/r_objects/gain8q24/de_genes/CBS.rds
    Untracked:  output/figures/r_objects/gain8q24/de_genes/FAM160B2.rds
    Untracked:  output/figures/r_objects/gain8q24/de_genes/FAM85B.rds
    Untracked:  output/figures/r_objects/gain8q24/de_genes/IGLV1-51.rds
    Untracked:  output/figures/r_objects/gain8q24/de_genes/MTERF3.rds
    Untracked:  output/figures/r_objects/gain8q24/de_genes/RPL23AP53.rds
    Untracked:  output/figures/r_objects/gain8q24/de_genes/TM6SF1.rds
    Untracked:  output/figures/r_objects/gain8q24/de_genes/TMEM242.rds
    Untracked:  output/figures/r_objects/gain8q24/de_genes/ZNF662.rds
    Untracked:  output/figures/r_objects/gain8q24/gain8q24_enrichment_dn.rds
    Untracked:  output/figures/r_objects/gain8q24/gain8q24_enrichment_up.rds
    Untracked:  output/figures/r_objects/med12/de_genes/C10orf105.rds
    Untracked:  output/figures/r_objects/med12/de_genes/COL1A1.rds
    Untracked:  output/figures/r_objects/med12/de_genes/DUSP2.rds
    Untracked:  output/figures/r_objects/med12/de_genes/ENTPD4.rds
    Untracked:  output/figures/r_objects/med12/de_genes/ERRFI1.rds
    Untracked:  output/figures/r_objects/med12/de_genes/HSPA1A.rds
    Untracked:  output/figures/r_objects/med12/de_genes/HSPA1B.rds
    Untracked:  output/figures/r_objects/med12/de_genes/HSPA6.rds
    Untracked:  output/figures/r_objects/med12/de_genes/IGHJ2P.rds
    Untracked:  output/figures/r_objects/med12/de_genes/IGHV1-45.rds
    Untracked:  output/figures/r_objects/med12/de_genes/IGKV2-28.rds
    Untracked:  output/figures/r_objects/med12/de_genes/IGLV6-57.rds
    Untracked:  output/figures/r_objects/med12/de_genes/LTBP1.rds
    Untracked:  output/figures/r_objects/med12/de_genes/MTUS1.rds
    Untracked:  output/figures/r_objects/med12/de_genes/RASSF1.rds
    Untracked:  output/figures/r_objects/med12/de_genes/SNCAIP.rds
    Untracked:  output/figures/r_objects/med12/de_genes/TMPRSS11E.rds
    Untracked:  output/figures/r_objects/med12/de_genes/TRIM16L.rds

Unstaged changes:
    Modified:   analysis/ATM.Rmd
    Modified:   analysis/Del8p12.Rmd
    Modified:   analysis/Med12.Rmd
    Modified:   output/de_genes_all.xlsx
    Modified:   output/enrichment/del11q22.3_gsea.rds
    Modified:   output/figures/paper_fig/figure_epi.pdf
    Modified:   output/figures/paper_fig/figure_epi.svg
    Modified:   output/figures/paper_fig/generate_figures.Rmd
    Modified:   output/figures/r_objects/BRAF/BRAF_enrichment_dn.rds
    Modified:   output/figures/r_objects/BRAF/BRAF_enrichment_up.rds
    Modified:   output/figures/r_objects/BRAF/BRAF_heatmap.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/ARHGEF37.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/BIRC5.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/CA1.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/CELSR2.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/DHRS9.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/DSP.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/F12.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/FAM111B.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/FAM184A.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/FAM96AP2.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/FLT4.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/HCAR1.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/HJURP.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/IGHV3-11.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/IGHV3-21.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/IGHV3-23.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/IGHV4-61.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/IQGAP3.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/KIF14.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/KIF18B.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/LINC00658.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/LINC01203.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/LINC01358.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/MELK.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/NRP2.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/OR2B6.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/PKMYT1.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/PLIN5.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/PPP1R14C.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/PPP1R3C.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/PTPRB.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/RNF157.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/RPSAP69.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/SAMD12.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/SDC3.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/SEPT3.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/SERPINE2.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/SH3RF1.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/SLC38A11.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/SPRY4.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/TFEC.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/TMEM151B.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/TMPRSS3.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/TSHZ2.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/ZFHX4.rds
    Modified:   output/figures/r_objects/BRAF/de_genes/ZNF503-AS1.rds
    Modified:   output/figures/r_objects/Notch1/de_genes/CLN8.rds
    Modified:   output/figures/r_objects/Notch1/de_genes/COL5A2.rds
    Modified:   output/figures/r_objects/Notch1/de_genes/GJB7.rds
    Modified:   output/figures/r_objects/Notch1/de_genes/IGLC6.rds
    Modified:   output/figures/r_objects/Notch1/de_genes/IGLV7-46.rds
    Modified:   output/figures/r_objects/Notch1/de_genes/KLK4.rds
    Modified:   output/figures/r_objects/Notch1/de_genes/MSI2.rds
    Modified:   output/figures/r_objects/Notch1/de_genes/NOTCH4.rds
    Modified:   output/figures/r_objects/Notch1/de_genes/SEPT3.rds
    Modified:   output/figures/r_objects/Notch1/de_genes/SPACA9.rds
    Modified:   output/figures/r_objects/Notch1/notch1_heatmap.rds
    Modified:   output/figures/r_objects/SF3B1/enrich_dot2.rds
    Modified:   output/figures/r_objects/SF3B1/enrich_net_hm.rds
    Modified:   output/figures/r_objects/SF3B1/enrich_net_kegg.rds
    Modified:   output/figures/r_objects/TP53/enrich_dot2.rds
    Modified:   output/figures/r_objects/TP53/enrich_net_hm.rds
    Modified:   output/figures/r_objects/TP53/enrich_net_kegg.rds
    Modified:   output/figures/r_objects/atm/atm_heatmap.rds
    Modified:   output/figures/r_objects/atm/de_genes/AHRR.rds
    Modified:   output/figures/r_objects/atm/de_genes/MECOM.rds
    Modified:   output/figures/r_objects/atm/de_genes/P4HA2.rds
    Modified:   output/figures/r_objects/atm/de_genes/PLCB1.rds
    Modified:   output/figures/r_objects/atm/de_genes/RBFOX2.rds
    Modified:   output/figures/r_objects/atm/de_genes/RNASE1.rds
    Modified:   output/figures/r_objects/atm/de_genes/SAXO2.rds
    Modified:   output/figures/r_objects/atm/de_genes/TMC5.rds
    Modified:   output/figures/r_objects/atm/de_genes/WNK2.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/ACAT1.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/AIRE.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/ALG9.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/ALKBH8.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/ATM.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/C11orf57.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/CUL5.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/CWF19L2.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/DDX10.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/DPY19L2.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/IGHV3-11.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/IGHV4-34.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/IGHV4-39.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/KBTBD3.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/NPAT.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/NT5E.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/PPP2R1B.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/RBM7.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/REXO2.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/SIK2.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/TEAD1.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/TMPRSS5.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/TTC12.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/USP28.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/ZW10.rds
    Modified:   output/figures/r_objects/del11q22/del11q22_enrichment_dn.rds
    Modified:   output/figures/r_objects/del11q22/del11q22_enrichment_up.rds
    Modified:   output/figures/r_objects/del11q22/del11q22_heatmap.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/ANK3.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/AXL.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/C10orf10.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/C1orf127.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/C9orf139.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/CD1A.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/CDCP1.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/CELSR2.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/CLEC4A.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/CNFN.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/CTAGE9.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/ENPP3.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/F12.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/IGHV1-24.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/IGHV3-23.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/IGHV3-49.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/IGKV2-24.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/IGKV4-1.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/IGLV1-40.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/IGLV3-10.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/ILDR2.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/ISL2.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/ITM2B.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/KCNRG.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/KIAA1549.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/KIF7.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/LARGE1.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/LINC00470.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/LINC00861.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/LINC02363.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/MAF.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/MIOX.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/MOGAT2.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/MTCO3P40.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/MTUS1.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/MYLK.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/NT5E.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/PALD1.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/PERP.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/PI16.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/PLEKHG7.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/RAMP1.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/RGL3.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/SCIN.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/SDC3.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/SERPINE2.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/SLC1A6.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/SMAD3.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/SNTB1.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/SOAT2.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/TFCP2L1.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/TM6SF1.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/TMPRSS4.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/TSPAN13.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/UACA.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/UBE2F.rds
    Modified:   output/figures/r_objects/del13q14/del13q14_heatmap.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/ACAP1.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/ANKRD36BP2.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/BTBD18.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/CA1.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/CDHR1.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/CPT1C.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/CTC1.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/CTNS.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/DPH1.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/DRC3.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/DSE.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/DVL2.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/FOXA3.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/FXR2.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/GK3P.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/GLOD4.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/GPS2.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/IGKV2-24.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/IGKV2D-28.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/IGLV9-49.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/KIAA0753.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/MAP2K4.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/MELK.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/MPDU1.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/MT-RNR1.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/MTMR11.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/MYH3.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/NEURL4.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/NLRP1.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/RABEP1.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/RNF167.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/SENP3.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/SMG6.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/SOX15.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/TNK1.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/TRPC5.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/UPK1A.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/VPS53.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/WRAP53.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/ZBTB4.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/ZZEF1.rds
    Modified:   output/figures/r_objects/del17p13/del17p13_heatmap.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/ADGRG7.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/ALG1L13P.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/C8orf58.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/DDX43.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/ELP3.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/EPHX2.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/ERICH1.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/FAM160B2.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/FBXO25.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/GTF2E2.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/HMBOX1.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/IGKV1-5.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/IGKV3-20.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/INTS10.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/INTS9.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/KIF13B.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/LGSN.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/LINC01016.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/MAPRE3.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/MCPH1.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/MEF2B.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/MTCO3P12.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/NEIL2.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/OVCH1.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/PNOC.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/PPP3CC.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/PRDM16.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/PSPHP1.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/PTCH1.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/PTK2B.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/PTP4A3.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/PTPRQ.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/R3HCC1.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/REEP4.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/SCUBE2.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/SLC44A5.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/SLC6A9.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/SNTB1.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/TRPM2-AS.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/XPO7.rds
    Modified:   output/figures/r_objects/del8p12/del8p12_heatmap.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/ABLIM2.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/BCL2A1.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/CAMK2N1.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/CHAD.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/CRIM1.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/E2F2.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/EBF1.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/EBF4.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/EML6.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/ENPP3.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/EPHB1.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/EPHB6.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/FAM212A.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/FGD6.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/FGF2.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/GEN1.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/GP5.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/JAG1.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/LEF1.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/PPP1R14A.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/RAI14.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/SLC4A8.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/SYBU.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/TCTN1.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/TIMELESS.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/TMPRSS11E.rds
    Modified:   output/figures/r_objects/epistasis/enrich_dot2.rds
    Modified:   output/figures/r_objects/epistasis/enrich_dot_buffering.rds
    Modified:   output/figures/r_objects/epistasis/enrich_dot_hm.rds
    Modified:   output/figures/r_objects/epistasis/enrich_dot_inversion.rds
    Modified:   output/figures/r_objects/epistasis/enrich_dot_supression.rds
    Modified:   output/figures/r_objects/epistasis/enrich_dot_synergy.rds
    Modified:   output/figures/r_objects/epistasis/enrich_net_kegg.rds
    Modified:   output/figures/r_objects/epistasis/epistasis_heatmap.rds
    Modified:   output/figures/r_objects/epistasis/epistasis_scheme.rds
    Modified:   output/figures/r_objects/epistasis/epistasis_scheme_lolli.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/ADAMDEC1.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/ALG1L13P.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/C8orf33.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/C8orf76.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/CPQ.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/CTHRC1.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/CYHR1.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/E2F5.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/EBAG9.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/FAM49B.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/FAM86B3P.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/IGKV3-20.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/INTS9.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/MTBP.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/PABPC1.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/PHF20L1.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/PLCD3.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/POLR2K.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/POTEM.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/PTPRQ.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/RAD21.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/RRM2B.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/SLC44A5.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/SNTB1.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/TATDN1.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/TMEM55A.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/TSTA3.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/UST.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/UTP23.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/ZNF16.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/ZNF251.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/ZNF462.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/ZNF7.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/ZNF706.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/ZNF707.rds
    Modified:   output/figures/r_objects/gain8q24/gain8q24_heatmap.rds
    Modified:   output/figures/r_objects/ighv/de_genes/ADAM29.rds
    Modified:   output/figures/r_objects/ighv/de_genes/ADAMTS7.rds
    Modified:   output/figures/r_objects/ighv/de_genes/ATOX1.rds
    Modified:   output/figures/r_objects/ighv/de_genes/BCAT1.rds
    Modified:   output/figures/r_objects/ighv/de_genes/C1orf106.rds
    Modified:   output/figures/r_objects/ighv/de_genes/CD38.rds
    Modified:   output/figures/r_objects/ighv/de_genes/CDHR1.rds
    Modified:   output/figures/r_objects/ighv/de_genes/CLEC9A.rds
    Modified:   output/figures/r_objects/ighv/de_genes/CPNE8.rds
    Modified:   output/figures/r_objects/ighv/de_genes/DGKH.rds
    Modified:   output/figures/r_objects/ighv/de_genes/DNAH14.rds
    Modified:   output/figures/r_objects/ighv/de_genes/DPY19L2.rds
    Modified:   output/figures/r_objects/ighv/de_genes/EGR3.rds
    Modified:   output/figures/r_objects/ighv/de_genes/FARP1.rds
    Modified:   output/figures/r_objects/ighv/de_genes/FGFR1.rds
    Modified:   output/figures/r_objects/ighv/de_genes/FRMD4B.rds
    Modified:   output/figures/r_objects/ighv/de_genes/GFI1.rds
    Modified:   output/figures/r_objects/ighv/de_genes/IGLC6.rds
    Modified:   output/figures/r_objects/ighv/de_genes/IGLV3-19.rds
    Modified:   output/figures/r_objects/ighv/de_genes/KANK2.rds
    Modified:   output/figures/r_objects/ighv/de_genes/KCNK9.rds
    Modified:   output/figures/r_objects/ighv/de_genes/LDOC1.rds
    Modified:   output/figures/r_objects/ighv/de_genes/LPL.rds
    Modified:   output/figures/r_objects/ighv/de_genes/MAPK4.rds
    Modified:   output/figures/r_objects/ighv/de_genes/MSI2.rds
    Modified:   output/figures/r_objects/ighv/de_genes/MYL12BP2.rds
    Modified:   output/figures/r_objects/ighv/de_genes/MYLK.rds
    Modified:   output/figures/r_objects/ighv/de_genes/NETO1.rds
    Modified:   output/figures/r_objects/ighv/de_genes/NFAT5.rds
    Modified:   output/figures/r_objects/ighv/de_genes/NPTX1.rds
    Modified:   output/figures/r_objects/ighv/de_genes/NUGGC.rds
    Modified:   output/figures/r_objects/ighv/de_genes/PEG10.rds
    Modified:   output/figures/r_objects/ighv/de_genes/PLD1.rds
    Modified:   output/figures/r_objects/ighv/de_genes/PLEKHG4B.rds
    Modified:   output/figures/r_objects/ighv/de_genes/PRR18.rds
    Modified:   output/figures/r_objects/ighv/de_genes/SEPT10.rds
    Modified:   output/figures/r_objects/ighv/de_genes/SLC12A1.rds
    Modified:   output/figures/r_objects/ighv/de_genes/SLC16A9.rds
    Modified:   output/figures/r_objects/ighv/de_genes/SOWAHC.rds
    Modified:   output/figures/r_objects/ighv/de_genes/VSIG10.rds
    Modified:   output/figures/r_objects/ighv/de_genes/WSB2.rds
    Modified:   output/figures/r_objects/ighv/de_genes/ZAP70.rds
    Modified:   output/figures/r_objects/ighv/de_genes/ZNF334.rds
    Modified:   output/figures/r_objects/ighv/enrich_dot2.rds
    Modified:   output/figures/r_objects/ighv/enrich_dot_hm.rds
    Modified:   output/figures/r_objects/ighv/enrich_net_hm.rds
    Modified:   output/figures/r_objects/ighv/enrich_net_kegg.rds
    Modified:   output/figures/r_objects/ighv/ighv_gene_status.rds
    Modified:   output/figures/r_objects/ighv/ighv_heatmap.rds
    Modified:   output/figures/r_objects/med12/de_genes/ADGRG7.rds
    Modified:   output/figures/r_objects/med12/de_genes/CDH20.rds
    Modified:   output/figures/r_objects/med12/de_genes/CLCNKA.rds
    Modified:   output/figures/r_objects/med12/de_genes/CSPG5.rds
    Modified:   output/figures/r_objects/med12/de_genes/DCHS1.rds
    Modified:   output/figures/r_objects/med12/de_genes/DDX43.rds
    Modified:   output/figures/r_objects/med12/de_genes/FCRL4.rds
    Modified:   output/figures/r_objects/med12/de_genes/FXYD6.rds
    Modified:   output/figures/r_objects/med12/de_genes/IGLV1-40.rds
    Modified:   output/figures/r_objects/med12/de_genes/IL15.rds
    Modified:   output/figures/r_objects/med12/de_genes/MTA1.rds
    Modified:   output/figures/r_objects/med12/de_genes/MYO5C.rds
    Modified:   output/figures/r_objects/med12/de_genes/NRCAM.rds
    Modified:   output/figures/r_objects/med12/de_genes/TCTN1.rds
    Modified:   output/figures/r_objects/med12/med12_heatmap.rds
    Modified:   output/figures/r_objects/summary_de_genes_IGHV_tri12.rds
    Modified:   output/figures/r_objects/summary_de_genes_all.rds
    Modified:   output/figures/r_objects/summary_var_freq_IGHV.rds
    Modified:   output/figures/r_objects/summary_variant_patient.rds

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.

File	Version	Author	Date	Message
html	712d2e9	aluetge	2019-11-19	Build site.
Rmd	a132f77	aluetge	2019-11-19	wflow_publish(c(“analysis/epistasis.Rmd”, “analysis/Gain8q24.Rmd”, “analysis/general_eda.Rmd”, “analysis/Med12.Rmd”))
html	6a79d5c	aluetge	2019-11-17	Build site.
Rmd	6c5aabc	aluetge	2019-11-17	wflow_publish(“analysis/general_eda.Rmd”)

Hierarchical structure

Find variables that explain the data#s structure in ansupervised way using hierarchical clustering and Principal component analysis

suppressPackageStartupMessages({
  library(DESeq2)
  library(dplyr)
  library(ggplot2)
  library(tidyverse)
  library(ComplexHeatmap)
  library(ggpubr)
  library(RColorBrewer)
  library(circlize)
  library(here)
})

Data

data_dir <- here("data")
output_dir <- here("output")
figure_dir <- here("output/figures")

#dds data set. gene expression data + patmetadata
load(paste0(data_dir, "/ddsrnaCLL_150218.RData"))

#load meta data including genotyping info
load(paste0(data_dir, "/patmeta_170324.RData"))

normalize data

#Variance stabilization transformation of the raw data
ddsCLL <- estimateSizeFactors(ddsCLL)
RNAnorm <- varianceStabilizingTransformation(ddsCLL, blind=T)

Filter genes

exprMat <- assay(RNAnorm)

# filter IG genes
filtered <- as_tibble(rowData(ddsCLL)) %>% mutate(geneID = rownames(ddsCLL)) %>% filter(!grepl("IGH",symbol)) %>% filter(!grepl("IGK",symbol)) %>% filter(!grepl("IGL",symbol))  

exprMat <- exprMat[filtered$geneID,]

#top 500 most variant genes
sds <- rowSds(exprMat)
exprMat <- exprMat[order(sds, decreasing = T)[1:500],]
colnames(exprMat) <- colData(ddsCLL)$PatID
exprMat.new <- log2(exprMat)
exprMat.new <- t(scale(t(exprMat.new)))
exprMat.new[exprMat.new > 4] <- 4
exprMat.new[exprMat.new < -4] <- -4
rownames(exprMat.new) <- rowData(RNAnorm[rownames(exprMat),])$symbol

Hierarchical clustering - heatmap

#colors
colors = colorRamp2(c(-4, -1 ,0, 1, 4), c("#2166ac","#4393c3", "#f7f7f7", "#d6604d","#b2182b"))
annocol <- get_palette("jco", 10)
annocolor <- list(IGHV = c("M" = annocol[1], "U" = annocol[2]) , 
                  trisomy12 = c( "1" = annocol[8], "0" = annocol[4]), 
                  Methylation = c("IP" = annocol[5], "LP" = annocol[6], "HP" =  annocol[7]))


# Annotations
#Top annotations
ha_top = HeatmapAnnotation(df = data.frame(colData(RNAnorm)[, c("IGHV", "trisomy12", "Methylation")]), 
                           col = annocolor, annotation_width = unit(c(rep(4, 3)), "cm"), 
                           show_legend = FALSE, 
                           simple_anno_size = unit(0.9, "cm"),
                           annotation_name_gp = gpar(fontsize = 20),
                           annotation_legend_param = list(title_gp = gpar(fontsize = 70), 
                                                          labels_gp = gpar(fontsize = 55),  
                                                          grid_height = unit(3, "cm"), 
                                                          grid_width = unit(1.5, "cm"), 
                                                          gap = unit(2, "cm")))

# Annotration legend
anno_legend_list = lapply(ha_top@anno_list[c("IGHV", "trisomy12", "Methylation")], function(anno){
  color_mapping_legend(anno@color_mapping, plot = FALSE,
                       title_gp = gpar(fontsize = 20, fontface = "bold"),
                       grid_height = unit(0.7, "cm"),
                       grid_width = unit(0.3, "cm"),
                       labels_gp = gpar(fontsize = 15))
  })

#Annotate known genes from litertaure
marker_genes <- c("ADAM29", "ATM", "CLLU1", "DMD", "GLO1", "HCSL1", "KIAA0977", 
                  "LPL", "MGC9913", "PCDH9", "PEG10", "SEPT10", "TCF7", "TCL1", 
                  "TP53", "VIM", "ZAP70", "CD38")

geneIDs <- which(rownames(exprMat.new) %in% marker_genes)
labels <- rownames(exprMat.new)[geneIDs]
ha_genes <- rowAnnotation(link = row_anno_link(at = geneIDs, 
                                               labels = labels, 
                                               labels_gp = gpar(fontsize = 20)), 
                          width = unit(2.5, "cm"))

Warning: anno_link() is deprecated, please use anno_mark() instead.

h1 <- Heatmap(exprMat.new ,                                                     
              km = 3,
              gap = unit(0.5, "cm"),
              clustering_distance_columns = "euclidean",
              clustering_method_columns = "ward.D2",
              clustering_distance_rows = "pearson",
              clustering_method_rows = "ward.D2",                    
              col = colors,
              column_title_gp = gpar(fontsize = 60, fontface = "bold"), 
              column_dend_height = unit(2.5, "cm"),
              show_row_dend = FALSE, 
              show_column_names = FALSE , 
              show_row_names = FALSE, 
              row_names_gp = gpar(fontsize = 45),
              show_heatmap_legend = FALSE,
              top_annotation = ha_top)

heatmap_legend = color_mapping_legend(h1@matrix_color_mapping, plot = FALSE, 
                                      title = "Expr", title_gp = gpar(fontsize = 20, fontface = "bold"),
                                      grid_height = unit(0.7, "cm"),
                                      grid_width = unit(0.3, "cm"),
                                      labels_gp = gpar(fontsize = 15))


# arrange annotations 
pd = packLegend(anno_legend_list[[1]], anno_legend_list[[2]], anno_legend_list[[3]], heatmap_legend, max_height = unit(20, "cm"), 
    column_gap = unit(0.5, "cm"))

pdf(file=paste0(output_dir, "/cluster500exprgenes.pdf"), width=20, height=20)
draw(h1, heatmap_legend_list = pd)
dev.off()

png 
  2

p1 <- draw(h1, heatmap_legend_list = pd)

Version	Author	Date
712d2e9	aluetge	2019-11-19
6a79d5c	aluetge	2019-11-17

#save to create figure using cowplot 
saveRDS(p1, paste0(output_dir, "/figures/r_objects/heatmap_top500genes.rds"))

Principal component analysis

#Plot PCA
exprMat <- assay(RNAnorm)

#top 5000 most variant genes
sds <- rowSds(exprMat)
na_ids <- which(is.na(ddsCLL$IGHV) | is.na(ddsCLL$trisomy12) | is.na(ddsCLL$Methylation))
exprMat <- exprMat[order(sds, decreasing = T)[1:500], -na_ids]


#Calculate PCA
pcaRes <- prcomp(t(exprMat), scale =T)
varExp <- (pcaRes$sdev^2 / sum(pcaRes$sdev^2)) * 100
pcaTab <- data.frame(pcaRes$x[,c(1:10)])
names(varExp) <- colnames(pcaRes$x)

#add background information
pcaTab <- cbind(pcaTab, data.frame(colData(RNAnorm)[-na_ids, ]))

#IGHV
p <- ggscatter(pcaTab, x = "PC1", y = "PC2", color = "IGHV", palette = "jco", size = 3,
  ylab = sprintf("PC2 (%2.1f%%)",varExp[2]), xlab = sprintf("PC1 (%2.1f%%)",varExp[1]), 
  legend = "right", main = "PCA coloured by IGHV status", 
  font.legend = c(23, "plain", "black"), 
  font.tickslab = c(23, "plain", "black"), 
  font.main = 25, font.submain = 28, font.caption = 28, font.x = 28, font.y= 28) + 
  coord_fixed()

p

Version	Author	Date
6a79d5c	aluetge	2019-11-17

#Tri12
p1 <- ggscatter(pcaTab, x = "PC1", y = "PC2", color = "trisomy12", size = 3,
  ylab = sprintf("PC2 (%2.1f%%)",varExp[2]), xlab = sprintf("PC1 (%2.1f%%)",varExp[1]), 
  legend = "right", main = "PCA coloured by trisomy12", 
  font.legend = c(23, "plain", "black"), 
  font.tickslab = c(23, "plain", "black"), 
  font.main = 25, font.submain = 28, font.caption = 28, font.x = 28, font.y= 28) + 
  coord_fixed() + 
  scale_colour_manual(values = c(annocol[4], annocol[8]))

p1

Version	Author	Date
6a79d5c	aluetge	2019-11-17

#Methylation
p2 <- ggscatter(pcaTab, x = "PC1", y = "PC2", color = "Methylation", size = 3,
  ylab = sprintf("PC2 (%2.1f%%)",varExp[2]), xlab = sprintf("PC1 (%2.1f%%)",varExp[1]), 
  legend = "right", main = "PCA coloured by Methylation", 
  font.legend = c(23, "plain", "black"), 
  font.tickslab = c(23, "plain", "black"), 
  font.main = 25, font.submain = 28, font.caption = 28, font.x = 28, font.y= 28) + 
  coord_fixed() + 
  scale_colour_manual(values = c(annocol[7], annocol[5], annocol[6]))

p2

Version	Author	Date
6a79d5c	aluetge	2019-11-17

#Methylation reduced gene number
#change gene number only 300 top variant genes
#Plot PCA
exprMat <- assay(RNAnorm)

#top 5000 most variant genes
sds <- rowSds(exprMat)
na_ids <- which(is.na(ddsCLL$Methylation))
exprMat <- exprMat[order(sds, decreasing = T)[1:300], -na_ids]


#Calculate PCA
pcaRes <- prcomp(t(exprMat), scale =T)
varExp <- (pcaRes$sdev^2 / sum(pcaRes$sdev^2)) * 100
pcaTab <- data.frame(pcaRes$x[,c(1:10)])
names(varExp) <- colnames(pcaRes$x)

#add background information
pcaTab <- cbind(pcaTab, data.frame(colData(RNAnorm)[-na_ids, ]))

p3 <- ggscatter(pcaTab, x = "PC1", y = "PC2", color = "Methylation", size = 3,
  ylab = sprintf("PC2 (%2.1f%%)",varExp[2]), xlab = sprintf("PC1 (%2.1f%%)",varExp[1]), 
  legend = "right", main = "PCA Methylation - top 300 genes", 
  font.legend = c(23, "plain", "black"), 
  font.tickslab = c(23, "plain", "black"), 
  font.main = 25, font.submain = 28, font.caption = 28, font.x = 28, font.y= 28) + 
  coord_fixed() + 
  scale_colour_manual(values = c(annocol[7], annocol[5], annocol[6]))

p3

Version	Author	Date
6a79d5c	aluetge	2019-11-17

saveRDS(list("IGHV" = p, "trisomy12" = p1, "Methylation" = p2, "Methylation_red_genes" = p3), 
        file = paste0(output_dir, "/figures/r_objects/pca_top500genes.rds"))

Hierachical clustering: Tree

library(dendextend)


---------------------
Welcome to dendextend version 1.13.4
Type citation('dendextend') for how to cite the package.

Type browseVignettes(package = 'dendextend') for the package vignette.
The github page is: https://github.com/talgalili/dendextend/

Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
Or contact: <tal.galili@gmail.com>

    To suppress this message use:  suppressPackageStartupMessages(library(dendextend))
---------------------


Attaching package: 'dendextend'

The following object is masked from 'package:ggpubr':

    rotate

The following object is masked from 'package:stats':

    cutree

library(corrplot)

corrplot 0.84 loaded

# Compute hierarchical clustering
exprMat <- assay(RNAnorm)

#top 5000 most variant genes
sds <- rowSds(exprMat)
exprMat <- exprMat[order(sds, decreasing = T)[1:500],]

sampleDists <- dist(t(exprMat)) 
sampleDistMat <- as.matrix(sampleDists)
rownames(sampleDistMat) <- colData(RNAnorm)$PatID


res.hc <- sampleDists %>% hclust(method = "ward.D2")
res.hc$labels <- ""    

##visualize with dendextend
mycols <-c( "#969696", "#525252", "#969696" , "#000000")
dend <-  as.dendrogram(res.hc) %>%
   set("branches_lwd", 2) %>% # Branches line width
   set("branches_k_color", mycols, k = 4)


#colormatrix
colMat <- matrix(nrow = ncol(RNAnorm), ncol = 3)
colMat[,1] <- ifelse(colData(RNAnorm)$IGHV == "M", annocol[1], annocol[2])
colMat[,2] <- ifelse(colData(RNAnorm)$trisomy12 == "1", annocol[8], annocol[4])
colMat[,3] <- ifelse(colData(RNAnorm)$Methylation == "HP", annocol[7], ifelse(colData(RNAnorm)$Methylation == "IP", annocol[5], annocol[6]))
colMat[which(is.na(colMat[,3])),3] <- "grey"

colnames(colMat) <- c("IGHV", "trisomy12", "Methylation")


plot(dend)
colored_bars(colMat, dend, rowLabels = c("IGHV", "trisomy12", "Methylation"), y_scale = 60, y_shift = 10, cex.rowLabels = 1)

## Check method's correspondence
# Create multiple dendrograms by chaining
dend1 <- sampleDists %>% hclust("complete") %>% as.dendrogram
dend2 <- sampleDists %>% hclust("ward.D2") %>% as.dendrogram
dend3 <- sampleDists %>% hclust("average") %>% as.dendrogram
dend4 <- sampleDists %>% hclust("centroid") %>% as.dendrogram
# Compute correlation matrix
dend_list <- dendlist("Complete" = dend1, "Ward.D2" = dend2,
                      "Average" = dend3, "Centroid" = dend4)
cors <- cor.dendlist(dend_list)
# Print correlation matrix
round(cors, 2)

         Complete Ward.D2 Average Centroid
Complete     1.00    0.71    0.80     0.25
Ward.D2      0.71    1.00    0.83     0.24
Average      0.80    0.83    1.00     0.41
Centroid     0.25    0.24    0.41     1.00

corrplot(cors, "pie", "lower")

C1C2 group signature

#get 1000 most variable genes
exprMat <- assay(RNAnorm)
sds <- rowSds(exprMat)
var500 <- rownames(exprMat[order(sds, decreasing = T)[1:500],])
var1000 <- rownames(exprMat[order(sds, decreasing = T)[1:1000],])
var5000 <- rownames(exprMat[order(sds, decreasing = T)[1:5000],])
var10000 <- rownames(exprMat[order(sds, decreasing = T)[1:10000],])

#Diff expressed gene list from Feirrera
c1c2_genes <- read.csv(paste0(data_dir, "/c1c2/Supplemental_File2_diffExpGenesC1C2_FC2.csv"), sep = ",",row.names = 1,header = TRUE)
exprMat_c <- assay(RNAnorm)
exprMat_c <- exprMat_c[which(rownames(RNAnorm) %in% rownames(c1c2_genes)),]
dim(exprMat_c)

[1] 602 184

#overlap var1000 and c1c2 genes
overlap_c1c2 <- list("top500" = var500,
                      "top1000" = var1000,
                      "top5000" = var5000,
                      "top10000" = var10000,
                      "all" = rownames(RNAnorm),
                      "c1c2" = rownames(c1c2_genes))

upset_mat <- list_to_matrix(overlap_c1c2 )
m = make_comb_mat(overlap_c1c2 )
comb_size(m)

000010 000001 000110 000011 001110 000111 011110 001111 111110 011111 
 20111     40   4837    194   3805    163    476    195    474     24 
111111 
    26

set_name(m)

[1] "top500"   "top1000"  "top5000"  "top10000" "all"      "c1c2"

UpSet(m)

#percentage category 
cat_vec <- rep("none", length(rownames(c1c2_genes)))
cat_vec[which(rownames(c1c2_genes) %in% var10000)] <- "top10000"
cat_vec[which(rownames(c1c2_genes) %in% var5000)] <- "top5000"
cat_vec[which(rownames(c1c2_genes) %in% var1000)] <- "top1000"
cat_vec[which(rownames(c1c2_genes) %in% var500)] <- "top500"
overlap_per <- data.frame("genes" = rownames(c1c2_genes),
                          "category" = cat_vec) 

overlap_per <- overlap_per %>% group_by(category) %>% summarize("overlap" = n())
overlap_per$category <- factor(overlap_per$category, levels = c("none", "top10000", "top5000", "top1000", "top500"))

p_c1c2 <- ggbarplot(overlap_per, "category", "overlap", 
                    fill = "category", 
                    palette = "uchicago", 
                    label = TRUE, 
                    lab.pos = "in", 
                    lab.col = "white",
                    title = "Overlap c1/c2 genes and top variable genes")

p_c1c2

#Plot expr mat
colnames(exprMat) <- colData(ddsCLL)$PatID
exprMat.new <- log2(exprMat_c)
exprMat.new <- t(scale(t(exprMat.new)))
exprMat.new[exprMat.new > 4] <- 4
exprMat.new[exprMat.new < -4] <- -4

# Annotations
#Top annotations
ha_top = HeatmapAnnotation(df = data.frame(colData(RNAnorm)[, c("IGHV", "trisomy12", "Methylation")]), 
                           col = annocolor, annotation_width = unit(c(rep(4, 3)), "cm"), 
                           show_legend = FALSE, 
                           simple_anno_size = unit(0.9, "cm"),
                           annotation_name_gp = gpar(fontsize = 20),
                           annotation_legend_param = list(title_gp = gpar(fontsize = 70), 
                                                          labels_gp = gpar(fontsize = 55),  
                                                          grid_height = unit(3, "cm"), 
                                                          grid_width = unit(1.5, "cm"), 
                                                          gap = unit(2, "cm")))

# Annotration legend
anno_legend_list = lapply(ha_top@anno_list[c("IGHV", "trisomy12", "Methylation")], function(anno){
  color_mapping_legend(anno@color_mapping, plot = FALSE,
                       title_gp = gpar(fontsize = 20, fontface = "bold"),
                       grid_height = unit(0.7, "cm"),
                       grid_width = unit(0.3, "cm"),
                       labels_gp = gpar(fontsize = 15))
  })

h1 <- Heatmap(exprMat.new ,                                                     
              km = 2,
              gap = unit(0.5, "cm"),
              clustering_distance_columns = "euclidean",
              clustering_method_columns = "ward.D2",
              clustering_distance_rows = "pearson",
              clustering_method_rows = "ward.D2",                    
              col = colors,
              column_title_gp = gpar(fontsize = 60, fontface = "bold"), 
              column_dend_height = unit(2.5, "cm"),
              show_row_dend = FALSE, 
              show_column_names = FALSE , 
              show_row_names = FALSE, 
              row_names_gp = gpar(fontsize = 45),
              show_heatmap_legend = FALSE,
              top_annotation = ha_top)

heatmap_legend = color_mapping_legend(h1@matrix_color_mapping, plot = FALSE, 
                                      title = "Expr", title_gp = gpar(fontsize = 20, fontface = "bold"),
                                      grid_height = unit(0.7, "cm"),
                                      grid_width = unit(0.3, "cm"),
                                      labels_gp = gpar(fontsize = 15))


# arrange annotations 
pd = packLegend(anno_legend_list[[1]], anno_legend_list[[2]], anno_legend_list[[3]], heatmap_legend, max_height = unit(20, "cm"), 
    column_gap = unit(0.5, "cm"))

draw(h1, heatmap_legend_list = pd)

Plot mean and sd of c1/c2 group

mean_c <- rowMeans(exprMat_c)
mean_all <- rowMeans(exprMat)
mean_top <- rowMeans(exprMat[var5000,])

sd_c <- rowSds(exprMat_c)
sd_all <- rowSds(exprMat)
sd_top <- rowSds(exprMat[var5000,])

cat_vec <- rep("none", length(rownames(exprMat)))
cat_vec[which(rownames(exprMat) %in% var10000)] <- "top10000"
cat_vec[which(rownames(exprMat) %in% var5000)] <- "top5000"
cat_vec[which(rownames(exprMat) %in% var1000)] <- "top1000"
cat_vec[which(rownames(exprMat) %in% var500)] <- "top500"
cat_vec[which(rownames(exprMat) %in% rownames(c1c2_genes))] <- "c1c2"
            

tab_all_cat <- data.frame("mean_count" = mean_all,
                          "sd_count" = sd_all,
                          "gene_category" = cat_vec)
  
  
p1 <- gghistogram(tab_all_cat, x = "mean_count",
   add = "mean", bins = 12, fill = "gene_category",
  palette = "uchicago")
p1

p2 <- gghistogram(tab_all_cat, x = "sd_count",
   add = "mean", bins = 12, fill = "gene_category",
  palette = "uchicago",
  title = "Standard deviation c1c2 genes compared to top variable genes")
p2

saveRDS(list("mean" = p1, "sd" = p2, "category" = p_c1c2), 
        file = paste0(output_dir, "/figures/r_objects/mean_sd_by_c1c2.rds"))

sessionInfo()

R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.7 LTS

Matrix products: default
BLAS:   /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8    
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8   
 [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
 [1] grid      parallel  stats4    stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:
 [1] corrplot_0.84               dendextend_1.13.4          
 [3] here_0.1                    circlize_0.4.6             
 [5] RColorBrewer_1.1-2          ggpubr_0.2                 
 [7] magrittr_1.5                ComplexHeatmap_2.0.0       
 [9] forcats_0.4.0               stringr_1.4.0              
[11] purrr_0.3.2                 readr_1.3.1                
[13] tidyr_0.8.3                 tibble_2.1.3               
[15] tidyverse_1.2.1             ggplot2_3.1.1              
[17] dplyr_0.8.1                 DESeq2_1.24.0              
[19] SummarizedExperiment_1.14.0 DelayedArray_0.10.0        
[21] BiocParallel_1.18.0         matrixStats_0.54.0         
[23] Biobase_2.44.0              GenomicRanges_1.36.0       
[25] GenomeInfoDb_1.20.0         IRanges_2.18.1             
[27] S4Vectors_0.22.0            BiocGenerics_0.30.0        

loaded via a namespace (and not attached):
 [1] colorspace_1.4-1       rjson_0.2.20           rprojroot_1.3-2       
 [4] htmlTable_1.13.1       XVector_0.24.0         GlobalOptions_0.1.0   
 [7] base64enc_0.1-3        fs_1.3.1               clue_0.3-57           
[10] rstudioapi_0.10        bit64_0.9-7            AnnotationDbi_1.46.0  
[13] lubridate_1.7.4        xml2_1.2.0             splines_3.6.3         
[16] geneplotter_1.62.0     knitr_1.23             Formula_1.2-3         
[19] jsonlite_1.6           workflowr_1.4.0        broom_0.5.2           
[22] annotate_1.62.0        cluster_2.1.1          png_0.1-7             
[25] compiler_3.6.3         httr_1.4.0             backports_1.1.4       
[28] assertthat_0.2.1       Matrix_1.3-2           lazyeval_0.2.2        
[31] cli_1.1.0              acepack_1.4.1          htmltools_0.3.6       
[34] tools_3.6.3            gtable_0.3.0           glue_1.3.1            
[37] GenomeInfoDbData_1.2.1 Rcpp_1.0.1             cellranger_1.1.0      
[40] nlme_3.1-152           xfun_0.7               rvest_0.3.4           
[43] XML_3.98-1.20          zlibbioc_1.30.0        scales_1.0.0          
[46] hms_0.4.2              yaml_2.2.0             memoise_1.1.0         
[49] gridExtra_2.3          rpart_4.1-15           latticeExtra_0.6-28   
[52] stringi_1.4.3          RSQLite_2.1.1          genefilter_1.66.0     
[55] checkmate_1.9.3        shape_1.4.4            rlang_0.3.4           
[58] pkgconfig_2.0.2        bitops_1.0-6           evaluate_0.14         
[61] lattice_0.20-38        labeling_0.3           htmlwidgets_1.3       
[64] bit_1.1-14             tidyselect_0.2.5       ggsci_2.9             
[67] plyr_1.8.4             R6_2.4.0               generics_0.0.2        
[70] Hmisc_4.2-0            DBI_1.0.0              pillar_1.4.1          
[73] haven_2.1.0            whisker_0.3-2          foreign_0.8-76        
[76] withr_2.1.2            survival_2.44-1.1      RCurl_1.95-4.12       
[79] nnet_7.3-15            modelr_0.1.4           crayon_1.3.4          
[82] rmarkdown_1.13         viridis_0.5.1          GetoptLong_0.1.7      
[85] locfit_1.5-9.1         readxl_1.3.1           data.table_1.12.2     
[88] blob_1.1.1             git2r_0.25.2           digest_0.6.19         
[91] xtable_1.8-4           munsell_0.5.0          viridisLite_0.3.0

Hierarchical structure

almut

17 November 2019

Hierarchical structure

Hierarchical clustering - heatmap

Principal component analysis

Hierachical clustering: Tree

C1C2 group signature

Plot mean and sd of c1/c2 group