dot-prep_geo_files: Prep GEO files

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

Prep GEO files

Description

Generate flat files that are ready for processing from GEO "raw" data. Warning! Raw data is highly variable for gse supplementary files

Usage

.prep_geo_files(
  study,
  gef,
  meta_data,
  input_files,
  analysis_dir,
  verbose = FALSE,
  reload = FALSE
)

Arguments

study	study accession eg SDY269
gef	result of ISCon$getDataset("gene_expression_files") for one run.
meta_data	list of study-specific meta data
input_files	input file names
analysis_dir	path to analysis directory
verbose	print verbose logging statements?
reload	re-download files if already found in analysis_dir?

Value

path to raw, prepped input files. tsv for everyone except affy, which will be the path to CEL files.

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