filter.annotation: filter.annotation

In lutsik/DecompPipeline: Preparation pipeline for MeDeCom

Description

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

Usage

filter.annotation(rnb.set, snp = TRUE, snp.list, somatic = TRUE,
  context = TRUE, qual.filter = NULL, dist.snps = FALSE)

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.
context	Flag indicating if probes in non-CpG context are to be removed.
qual.filter	Vector of indices removed during quality filtering.
dist.snps	Flag indicating of potential SNPs are to be determined by selecting those sites that have trimodally distributed (differences 0, 0.5 and 1.0) pairwise differences across the samples.

Value

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

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