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,
  correct.switch = TRUE,
  mask.use.tcga = FALSE,
  pval.threshold = 0.05,
  pval.method = NULL,
  sum.TypeI = FALSE
)

Arguments

sset

SigSet

quality.mask

whether to mask low quality probes

nondetection.mask

whether to mask nondetection

correct.switch

whether to correct switch

mask.use.tcga

whether to use TCGA masking, only applies to HM450

pval.threshold

p-value threshold for nondetection mask

pval.method

method for detection threshold, like pOOBAH, PnegEcdf

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 1.6.0 Index]