filter.quality.covg: filter.quality.covg

In lutsik/DecompPipeline: Preparation pipeline for MeDeCom

Description

This functions filters the CpG sites in the given rnb.set for quality criteria specified in the arguments.

Usage

filter.quality.covg(rnb.set, min.covg, min.covg.quant = 0.05,
  max.covg.quant = 0.95)

Arguments

rnb.set	An object of type RnBSet-class containing the CpG sites used for filtering, all well as intensity and coverage informatio, if provided.
min.covg	Integer specifying the minimum number of beads required for including the site in the analysis.
min.covg.quant	Lower quantile of coverage which is to be removed.
max.covg.quant	Upper quantile of coverage which is to be removed.

Details

The probes with lower/higher coverage than min.int.quant/ max.int.quant are removed.

Value

The indices of the sites that are to be kept.

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