getProbeInfo {oligo}R Documentation

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.

Note

The code allows for querying info on MM probes, however it has been used mostly on PM probes.

Author(s)

Benilton Carvalho

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)
}

[Package oligo version 1.56.0 Index]