read.illumina.manifest: Import an Illumina manifest file

In drmjc/lumidat: Methods for importing Illumina gene expression iDAT files

Description

Import an Illumina manifest file. Only manifest files in TXT format are supported, ie, BGX files can't be read. These files can be downloaded from Illumina [1,2]

Usage

  read.illumina.manifest(f, verbose = FALSE)

Arguments

f	the path to the manifest file name
verbose	logical if “TRUE” print informative messages. Default “FALSE”.

Value

a list with 2 elements, probes and controls. Both elements are “data.frame”'s with as many columns as found in the manifest file

Author(s)

Mark Cowley, 2011-06-02

See Also

[1] http://www.switchtoi.com/annotationfiles.ilmn

[2] http://www.switchtoi.com/annotationprevfiles.ilmn

Examples

manifestfile <- system.file("extdata", "HumanHT-12_V3_0_R1_99999999.txt", package="lumidat")
manifest <- read.illumina.manifest(manifestfile, TRUE)
head(manifest$probes)
head(manifest$controls)

drmjc/lumidat documentation built on May 15, 2019, 2:23 p.m.