filter.annotation.biseq: filter.annotation.biseq

In lutsik/DecompPipeline: Preparation pipeline for MeDeCom

Description

This function removes sites in SNP or sex-chromosomal context.

Usage

filter.annotation.biseq(rnb.set, snp = TRUE, snp.list, somatic = TRUE,
  qual.filter = NULL)

Arguments

rnb.set	An object of type RnBSet-class containg annotation information.
snp	Flag indicating if snps are to be removed. Either SNPs annotated in the RnBeads annotation object of specified as an additional file with one SNP identifier per row in snp.list.
snp.list	Path to a file containing known SNPs. One SNP identifier should be present per row.
somatic	Flag indicating if only somatic probes are to be kept.
qual.filter	Vector of indices removed during quality filtering.

Details

This functions uses information on the sites on the chip and transfers this knowledge to BS data sets.

Value

A vector of indices of sites surviving the annotation filter criteria.

lutsik/DecompPipeline documentation built on Oct. 13, 2019, 1:51 a.m.