getBetas {sesame} | R Documentation |
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.
getBetas(sset, quality.mask = TRUE, nondetection.mask = TRUE, mask.use.tcga = FALSE, pval.threshold = 0.05, sum.TypeI = FALSE)
sset |
|
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 |
a numeric vector, beta values
sset <- sesameDataGet('EPIC.1.LNCaP')$sset betas <- getBetas(sset)