filter.quality: filter.quality

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(rnb.set, beads = TRUE, min.beads, intensity = TRUE,
  min.int.quant = 0.1, max.int.quant = 0.95, subs)

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.
beads	Flag indicating if sites not having more than min.beads number of beads in all samples are to be removed.
min.beads	Integer specifying the minimum number of beads required for including the site in the analysis.
intensity	Flag indicating if sites are to be filtered according to their intensity information.
min.int.quant	Lower quantile of intensities which is to be removed.
max.int.quant	Upper quantile of intensities which is to be removed.
subs	Argument specifying the subset of samples to be used

Details

If intensity is set, those probes with lower/higher intensity in one of the channels 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.