getBetasTypeIbySumChannels {sesame}R Documentation

Get beta values treating type I by summing channels

Description

This function is used for rescuing beta values on Color-Channel-Switching CCS probes. The function takes a SigSet and returns beta value except that Type-I in-band signal and out-of-band signal are combined. This prevents color-channel switching due to SNPs.

Usage

getBetasTypeIbySumChannels(sset, quality.mask = TRUE,
  nondetection.mask = TRUE, pval.threshold = 0.05)

Arguments

sset

SigSet

quality.mask

whether to mask low quality probes

nondetection.mask

whether to mask nondetection

pval.threshold

p-value threshold for nondetection mask

Value

beta values

Examples

sset <- makeExampleSeSAMeDataSet()
betas <- getBetasTypeIbySumChannels(sset)

[Package sesame version 1.0.0 Index]