dot-make_id_to_gsm_map: Make id to GSM map

In RGLab/HIPCMatrix: Microarray and RNA-seq Processing for ImmuneSpace

Make id to GSM map

Description

Create map of GSM accessions to ID's provided in GSE. If needed, appropriate info for the matrix will be returned by get_meta_data.

Usage

.make_id_to_gsm_map(
  gsms,
  study_id_term,
  gsm_map_index = 1,
  id_regex_map = NULL,
  supp_files_dir = NULL
)

Arguments

gsms	Input vector of gsm accession
study_id_term	Term from getGEO(gsm) header to use for extracting sample id. "description" or "title"
gsm_map_index	Index returning id in GSM header
id_regex_map	list specifying regex terms to map GSE id's using gsub of the form list(old = "", new = "")
supp_files_dir	path to directory to save supplementary files.

RGLab/HIPCMatrix documentation built on Jan. 29, 2023, 5:13 a.m.