create_genes_gtrack: create_genes_gtrack

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

create_genes_gtrack

Description

zchoo Monday, Apr 26, 2021 02:24:31 PM

Usage

create_genes_gtrack(
  genes = c(),
  gencode.fname = NULL,
  coding.only = TRUE,
  level.thresh = 2,
  cached.dir = Sys.getenv("GENCODE_DIR")
)

Arguments

genes	(character vector) genes to mark using "label" GRangesList metadata column (all other genes will have label == NA)
gencode.fname	(character) path to GENCODE GFF
coding.only	(logical) only include entries with gene_type == 'protein_coding'
level.thresh	(numeric) only include entries with level <= level.thresh
cached.dir	(character) path to directory in which to save the output gTrack
verbose	(logical)

Value

file name of gencode gTrack

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