parseGEOSignalABFile: Parse GEO signal-A/B File into a SigSet List

In sesame: Tools For Analyzing Illumina Infinium DNA Methylation Arrays

Description

This function is meant to be a convenience function for parsing data from Signal_A and Signal_B file provided by GEO. In many cases, this function generates a "partial" SigSet due to lack of out-of-band signal and control probe measurement in those Signal_A/B files. The detection p-value is based on a fixed normal distribution rather than from negative control or OOB probes.

Usage

parseGEOSignalABFile(path, platform = "HM450", drop = TRUE, parallel = TRUE)

Arguments

path	path to Signal-A/B file downlaoded from GEO. The file can remain gzipped.
platform	HM450, EPIC or HM27
drop	whether to reduce to SigSet when there is only one sample.
parallel	whether to use multiple cores.

Value

a SigSetList or a SigSet

Examples

path = system.file(
    'extdata',
    'GSE36369_NonEBV_SignalA_SignalB_3samples_1k.txt.gz',
    package='sesame')
ssets <- parseGEOSignalABFile(path)

sesame documentation built on Nov. 15, 2020, 2:08 a.m.