Evolution of the nonsense mediated decay pathway is associated with decreased cytolytic immune infiltration.

Authors: Boyang Zhao and Justin Pritchard

File info for folder src

• analyze.R: random forest model building and analyses
• analyze_indv.R: individual ad-hoc analyses
• analyze_mod.R: additional analyses of the random forest model results
• analyze_pan.R: aggregate pan-cancer analyses
• analyze_nullmodel.R: random forest null model building
• analyze_nullmodel_results.R: analyze null model results
• analyze_indv_globalNMD.R: individual ad-hoc analyses, for global NMD
• analyze_indv_survivalSKCM.R: individual ad-hoc analyses, for SKCM survival
• nmd_compr.R: NMD alterations analyses, association with NMD metrics
• nmd_compr_triple.R: NMD alterations analyses, broken to compare none, 1, or >1 variants
• nmd_compr_cyt.R: NMD alterations analyses, association with cytolytic activity
• utils_surv.R: survival methods used for analyses
• utils.R: methods used for analyses

File info for folder datasets

The folders are organized by indication, and downloaded from Broad firehose.

• *_clin contains clinical data
• *_cna contains CNA data
• *_mut contains MAF mutational data
• *_rnaseq contains RNA-seq data

File info for folder outputs

• 18.0604: random forest model results
• 18.1212_survival: survival analyses. Parsed .rda files from 18.0604 were copied over to this folder, and survival analyses were then run
• 19.0108 cbio: genetic alterations of NMD and other pathways, results from cBioPortal
• 19.0108_cnacutoff_1_NMDpos_ampdel: cnv of genes in the NMD pathway across indications
• 19.0110_cnacutoff_1_NMDpos: association of NMD genes (any alterations) with NMD metrics, this is used for the subsequent analyses below
• 19.0110_cnacutoff_1_NMDpos_CooccurCyt: association of NMD co-alterations and cytolytic activity
• 19.0110_cnacutoff_1_NMDpos_CooccurVs1variantVsCtrl: trend analyses of NMD genetic alterations and NMD metrics
• 19.0110_cnacutoff_1_NMDpos_CooccurVsCtrl: association of NMD genes (co-alterations) with NMD metrics
• 19.0817_nullmodel: results from null model (randomized inputs)
• 19.0819_cox: residual results from Cox regression models
• 19.0820_NMDglobal: generate visualizations for NMD global differences plots