processGeneSignatureFiles: Read gene signature files for many experiments and merge them...

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

Read gene signature files for many experiments and merge them to a 'data.table'

Description

Read gene signature files for many experiments and merge them to a 'data.table'

Usage

processGeneSignatureFiles(
  filePath,
  mDataType = c("rna", "cnv", "mutation"),
  ...,
  keyColumns = c("gene", "compound", "tissue", "dataset", "mDataType"),
  fileFormats = c("rds", "qs"),
  logDir = "logs"
)

Arguments

filePath	'character(1)' Path to top level signature directory. This should contain a folder '<mDataType>'.
mDataType	'character(1)' The molecular data type of the signatures.
...	Fall through parameters to ['BiocParallel::bplapply']. These parameters contral internal function parallelization.
keyColumns	'character' Vector of column names in the signature file to join on. For developer use, do no change.
fileFormats	'character' Vector of file formats without a dot (e.g., rds)

Value

'data.table' The gene signatures properly formatted to a single long format table.

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