parseGEOSignalABFile {sesame} | R Documentation |
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.
parseGEOSignalABFile(path, platform = "HM450", drop = TRUE, parallel = TRUE)
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. |
a SigSetList or a SigSet
path = system.file( 'extdata', 'GSE36369_NonEBV_SignalA_SignalB_3samples_1k.txt.gz', package='sesame') ssets <- parseGEOSignalABFile(path)