Index-methods: Accessors for PM, MM or background probes indices.

In jmacdon/oligo: Preprocessing tools for oligonucleotide arrays

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

Details

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

Value

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

Examples

## How pm() works
## Not run: 
x <- read.celfiles(list.celfiles())
pms0 <- pm(x)
pmi <- pmindex(x)
pms1 <- exprs(x)[pmi,]
identical(pms0, pms1)

## End(Not run)

jmacdon/oligo documentation built on Aug. 11, 2020, 12:32 a.m.