compute_rna_quantiles: compute_rna_quantiles

In mskilab/casereport: casereport: Whole-genome + transcription based report for cancer genomes

compute_rna_quantiles

Description

Creates a data.table containing the expression level of each gene relative to a cohort. If supplied, also adds role of gene (e.g. ONC/TSG)

Usage

compute_rna_quantiles(
  tpm = NULL,
  tpm.cohort = NULL,
  onc = as.character(),
  tsg = as.character(),
  surface = as.character(),
  id = NULL,
  gencode.gtrack = NULL,
  quantile.thresh = 0.05,
  verbose = FALSE
)

Arguments

tpm	(character) path to file with RNA TPM input (can be kallisto, salmon, or prespecified format)
onc	(character) character vector of oncogenes
tsg	(character) character vector of TSGs
surface	(character) character vector of surface genes
id	(character) id of current sample
gencode.gtrack	(character) path to gencode gTrack
quantile.thresh	(numeric) default 0.05
verbose	(logical)
tpm_cohort	(character) path to file with cohort expression

Value

data.table with columns gene, pair, value, qt, role, and direction of over/under expression

mskilab/casereport documentation built on Oct. 19, 2022, 3 a.m.