detectionPnegNorm {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.
detectionPnegNorm(sset, pval.threshold = 0.05, return.pval = FALSE)
sset |
a |
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 negative control probes-parameterized normal distribution. p-value is taken from the minimum of the p-value of the two alleles (color depends on probe design).
a SigSet
, or a p-value vector if return.pval is TRUE
sset <- sesameDataGet("HM450.1.TCGA.PAAD")$sset sum(mask(sset)) sset_with_mask <- detectionPnegNorm(sset) sum(mask(sset_with_mask))