qualityMask {sesame}R Documentation

Mask beta values by design quality

Description

Currently quality masking only supports three platforms

Usage

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

Arguments

sdf

a SigDF object

mask.use.manifest

use manifest to mask probes

manifest

the manifest to use, for custom arrays

mask.use.tcga

whether to use TCGA masking, only applies to HM450

Value

a filtered SigDF

Examples

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

[Package sesame version 1.12.7 Index]