read.snpChip: Read in split Illumina snp chip files

In seandavi/Rpressa: A collection of useful code for bioinformatics

Description

Reads the SNP_Map.txt, Sample_Map.txt, and the one-sample-per-file export files from the GenomeStudio export.

Usage

read.snpChip(path='.',file.prefix,sampleMapFile=file.path(path,"Sample_Map.txt"),
           snpMapFile=file.path(path,"SNP_Map.txt"),...) {
}

Arguments

path	The string representing the path to the GenomeStudio export files.
file.prefix	The GenomeStudio export file prefix that will be prepended to the file names for each sample. In the end, the file names will be of the form "file.prefix##.txt" where "##" is the sample number.
sampleMapFile	The default will specify the default file name from the GenomeStudio output in the same directory as the exported data files. This file contains the sample annotations. The resulting data frame becomes the phenoData for the ExpressionSet.
SNPMapFile	The default will specify the default file name from the GenomeStudio output in the same directory as the exported data files. This file contains the SNP annotations and will end up in the featureData for the resulting ExpressionSet.
...	Passed to read.table()

Value

An "ExpressionSet" object.

Author(s)

Sean Davis <[e-mail]>

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

seandavi/Rpressa documentation built on May 29, 2019, 4:33 p.m.