fetch.expression.data: Fetch expression data from GEO / or given folder

In emreg00/pepper: PErsonalized Perturbation ProfilER

Description

Fetch expression data from GEO / or given folder

Usage

fetch.expression.data(geo.id, sample.mapping.column = "characteristics_ch1",
  do.log2 = NULL, probe.conversion = NULL, conversion.mapping = NULL,
  conversion.mapping.function = NULL, output.dir = getwd(),
  geo.id.sub = NULL, reprocess = NULL)

Arguments

geo.id	GEO id
sample.mapping.column	The column in the sample annotation that contains phenotype info (default: "characteristics_ch1")
do.log2	Apply log2 transformation to the expression values. If NULL (default), deduced from the data (code from GEO2R at NCBI)
probe.conversion	Convert probe level expression to gene level using provided annotation label (uses platform specific annotations downloaded from GEO) Defaults to NULL (no conversion). In case of multiple probes, probe with absolute max value is chosen
conversion.mapping	Mapping of platform specific ids to user provided ids
conversion.mapping.function	Function to process the mapped name such that it matches with the ids provided in conversion.map
output.dir	Directory where all files will be written (defaults to current working dir)
geo.id.sub	GEO id for the sub-set (e.g., specific to the platform)

Value

A list containing 3 data frames: expression matrix, sample mapping, gene mapping

Examples

gds.data = fetch.expression.data("GDS4966", do.log2=F, probe.conversion="Gene ID")
expr = gds.data$expr
sample.mapping = gds.data$sample.mapping

emreg00/pepper documentation built on May 16, 2019, 5:10 a.m.