parseGEOSoft: parse GO Soft archives

In raim/segmenTools: Tools for Functional Genome Exploration

parse GO Soft archives

Description

Parses GEO Soft microarray experiment archives into a data matrix and an ID-probe mapping table. Probes can be further summarized for features with summarizeGEOSoft.

Usage

parseGEOSoft(
  file,
  idcol,
  exp = 1,
  only.info = FALSE,
  only.data = TRUE,
  valcol = "VALUE",
  title = TRUE,
  desc = TRUE
)

Arguments

file	a GEO Soft archive file (eg. GSE18902_family.soft.gz)
idcol	columns to retrieve from the platform table
exp	number of the platform to retrieve from a GEO file with multiple platforms. TODO: allow to parse multiple platforms.
only.info	only parse information on probes and experiments, but skip the actual data
only.data	skip all samples without data
valcol	value column (currently only 1 is allowed) in the sample tables
title	if TRUE a sample title will be retrieved
desc	if TRUE, value descriptions in field "#<valcol>" will be retrieved

See Also

summarizeGEOSoft

raim/segmenTools documentation built on March 20, 2024, 6:23 a.m.