| pm-methods {xps} | R Documentation |
Methods for accessing perfect match (PM) and mismatch (MM) probes.
Usage
pm(object, which = "pm")
mm(object, which = "mm")
object |
object of class DataTreeSet. |
which |
type of perfect match or mismatch probes to be returned. |
For expression arrays all the perfect match (pm) or mismatch (mm) probes on the arrays the object represents are returned as data.frame.
For exon arrays, pm returns the probes of the different exon levels as data.frame,
i.e. which can have one of the following values:
core: | probesets supported by RefSeq and full-length GenBank transcripts. | |
metacore: | core meta-probesets. | |
extended: | probesets with other cDNA support. | |
metaextended: | extended meta-probesets. | |
full: | probesets supported by gene predictions only. | |
metafull: | full meta-probesets. | |
affx: | standard AFFX controls. |
For whole genome arrays, pm returns the probes of the different exon levels as data.frame,
i.e. which can have one of the following values:
core: | probesets with category ‘unique’ and ‘mixed’. | |
metacore: | probesets with category ‘unique’ only. | |
affx: | standard AFFX controls. |
For exon/genome arrays, mm returns the background probes as data.frame,
i.e. which is either “genomic” or “antigenomic”.
A data.frame.
Christian Stratowa
## load existing ROOT scheme file and ROOT data file
scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
data.test3 <- root.data(scheme.test3, paste(.path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))
## need to attach scheme mask and probe intensities
data.test3 <- attachMask(data.test3)
data.test3 <- attachInten(data.test3)
pm <- pm(data.test3)
mm <- mm(data.test3)
head(pm)
head(mm)
## optionally remove mask and data to free memory
data.test3 <- removeInten(data.test3)
data.test3 <- removeMask(data.test3)