oligo (version 1.36.1)

getProbeInfo: Probe information selector.

Description

A tool to simplify the selection of probe information, so user does not need to use the SQL approaches.

Usage

getProbeInfo(object, field, probeType = "pm", target = "core", sortBy = c("fid", "man_fsetid", "none"), ...)

Arguments

object

FeatureSet object.

field

character string with names of field(s) of interest to be obtained from database.

probeType

character string: 'pm' or 'mm'

target

Used only for Exon or Gene ST arrays: 'core', 'full', 'extended', 'probeset'.

sortBy

Field to be used for sorting.

...

Arguments to be passed to subset

Value

• A data.frame with the probe level information.

Examples

if (require(oligoData)){
   data(affyGeneFS)
   availProbeInfo(affyGeneFS)
   probeInfo <- getProbeInfo(affyGeneFS, c('fid', 'x', 'y', 'chrom'))
   head(probeInfo)
   ## Selecting antigenomic background probes
   agenGene <- getProbeInfo(affyGeneFS, field=c('fid', 'fsetid', 'type'), target='probeset', subset= type == 'control->bgp->antigenomic')
   head(agenGene)
}