oligo (version 1.36.1)

mmindex: Accessors for PM, MM or background probes indices.

Description

Extracts the indexes for PM, MM or background probes.

Usage

mmindex(object, ...)
pmindex(object, ...)
bgindex(object, ...)

Arguments

object

FeatureSet or DBPDInfo object

...

Extra arguments, not yet implemented

Value

• A vector of integers representing the rows of the intensity matrix that correspond to PM, MM or background probes.

Details

The indices are ordered by 'fid', i.e. they follow the order that the probes appear in the CEL/XYS files.

Examples

## How pm() works
x <- read.celfiles(list.celfiles())
pms0 <- pm(x)
pmi <- pmindex(x)
pms1 <- exprs(x)[pmi,]
identical(pms0, pms1)