curateExpdata: curateExpdata

Description Usage Arguments Value

View source: R/curateExpData.R

Description

This function will take the name lists generated by nameChange and apply them to an expression data set. The function will process locally downloaded GEO expression files, or even just accept a GEO accession number and do the work for you.

Usage

1
curateExpdata(expname, namelist, local = F, pct = 0.8, pullmeta = F)

Arguments

expname

This is the name of your data set; if local is T, it is a GEO file (any type containing exp data). If local is F, this can be a GEO accession number.

namelist

This is a name list file as generated by nameChange.

local

This is a logical variable; if T, the function looks for a local file. If F, the function uses the expname as a GEO accession number and attempts to download the data.

pct

This is the cutoff for gene data; if a gene has expression values for less than this percentage of samples, it is excluded.

pullmeta

This allows you to get the metadata for the samples from the GSE file; default is false.

Value

Returns an expression frame containing genes as rows and samples as columns. If pullmeta = T, will be a list with the first entry being the expression frame and the second being the metadata from a GSE file.


foster-gabe/PFExpTools documentation built on May 25, 2020, 7:22 a.m.