getBetasTypeIbySumChannels {sesame} | R Documentation |
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.
getBetasTypeIbySumChannels(sset, quality.mask = TRUE, nondetection.mask = TRUE, pval.threshold = 0.05)
sset |
|
quality.mask |
whether to mask low quality probes |
nondetection.mask |
whether to mask nondetection |
pval.threshold |
p-value threshold for nondetection mask |
beta values
sset <- makeExampleSeSAMeDataSet() betas <- getBetasTypeIbySumChannels(sset)