qualityMask {sesame}R Documentation

Mask beta values by design quality

Description

Currently quality masking only supports three platforms

Usage

qualityMask(
  sset,
  mask.use.manifest = TRUE,
  manifest = NULL,
  mask.use.tcga = FALSE
)

Arguments

sset

a SigSet object

mask.use.manifest

use manifest to mask probes

manifest

the manifest file that contains mask column

mask.use.tcga

whether to use TCGA masking, only applies to HM450

Value

a filtered SigSet

Examples

sesameDataCache("EPIC") # if not done yet
sset <- sesameDataGet('EPIC.1.LNCaP')$sset
sum(mask(sset))
sset.masked <- qualityMask(sset)
sum(mask(sset.masked))

[Package sesame version 1.10.5 Index]