readGeneSigsForPSet: Takes in the path to a set of gene signature .rds files,...

In bhklab/rPharmacoDI: PharmacoDB Data Ingestion - functions for converting pSets to PharmacoDB database tables

Takes in the path to a set of gene signature .rds files, selects those path matching 'pSetPattern' and converts them into a list of PharmacoSig objects.

Description

Takes in the path to a set of gene signature .rds files, selects those path matching 'pSetPattern' and converts them into a list of PharmacoSig objects.

Usage

readGeneSigsForPSet(
  dataDir,
  pSetPattern,
  mDataTypes,
  BPPARAM = BiocParallel::bpparam()
)

Arguments

dataDir	['character'] vector specifying the path to the gene signature .rds files
pSetPattern	['character'] an identifier for the Pset you wish to read. In general this will be the pSet indentifier (e.g., GDSC_v1). '.*' is automatically prepended and appended to the pattern, so adding this is not necssary.
mDataTypes	['character'] directory names for each molecular datatype to read gene signatures for.
BPPARAM	['BiocParam'] object specifying what backend to use for parallelization. This defaults to your registered back-end, retrieved via the 'BiocParallel::bpparam()' function.

Value

['list'] of 'PharmacoSig' objects for the selected pSet

bhklab/rPharmacoDI documentation built on Oct. 31, 2022, 11:06 a.m.