getBetas {sesame}R Documentation

Get beta Values

Description

sum.typeI 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

getBetas(sset, quality.mask = TRUE, nondetection.mask = TRUE,
  mask.use.tcga = FALSE, pval.threshold = 0.05, sum.TypeI = FALSE)

Arguments

sset

SigSet

quality.mask

whether to mask low quality probes

nondetection.mask

whether to mask nondetection

mask.use.tcga

whether to use TCGA masking, only applies to HM450

pval.threshold

p-value threshold for nondetection mask

sum.TypeI

whether to sum type I channels

Value

a numeric vector, beta values

Examples

sset <- sesameDataGet('EPIC.1.LNCaP')$sset
betas <- getBetas(sset)

[Package sesame version 1.2.0 Index]