pmFragmentLength: Access the fragment length for PM probes.

In jmacdon/oligo: Preprocessing tools for oligonucleotide arrays

Description

Accessor to the fragment length for PM probes.

Usage

pmFragmentLength(object, enzyme, type=c('snp', 'cn'))

Arguments

object	PDInfo or SnpFeatureSet object.
enzyme	Enzyme to be used for query. If missing, all enzymes are used.
type	Type of probes to be used: 'snp' for SNP probes; 'cn' for Copy Number probes.

Value

A list of length equal to the number of enzymes used for digestion. Each element of the list is a data.frame containing:

• row: the row used to link to the PM matrix;

• length: expected fragment length.

Note

There is not a 1:1 relationship between probes and expected fragment length. For one enzyme, a given probe may be associated to multiple fragment lengths. Therefore, the number of rows in the data.frame may not match the number of PM probes and the row column should be used to match the fragment length with the PM matrix.

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