detectionPfixedNorm {sesame} | R Documentation |
The function takes a SigSet
as input, computes detection p-value
using negative control probes parametrized in a normal distribution and
returns a new SigSet
with an updated pval slot.
detectionPfixedNorm( sset, muG = 500, sdG = 200, muR = 500, sdR = 200, pval.threshold = 0.05, return.pval = FALSE )
sset |
a |
muG |
mean of background in Grn channel |
sdG |
SD of background in Grn channel |
muR |
mean of background in Red channel |
sdR |
SD of background in Red channel |
pval.threshold |
minimum p-value to mask |
return.pval |
whether to return p-values, instead of a
masked |
Background of Grn and Red are estimated separately from a fixed normal distribution. p-value is taken from the minimum of the p-value of the two alleles (color depends on probe design).
detection p-value
sset <- sesameDataGet('HM450.1.TCGA.PAAD')$sset sum(mask(sset)) sset_with_mask <- detectionPfixedNorm(sset) sum(mask(sset_with_mask))