detectionPoobEcdf {sesame} | R Documentation |
aka pOOBAH (p-vals by Out-Of-Band Array Hybridization)
detectionPoobEcdf(sset, return.pval = FALSE, pval.threshold = 0.05) pOOBAH(sset, return.pval = FALSE, pval.threshold = 0.05)
sset |
a |
return.pval |
whether to return p-values, instead of a
masked |
pval.threshold |
minimum p-value to mask |
The function takes a SigSet
as input, computes detection p-value
using out-of-band probes empirical distribution and returns a new
SigSet
with an updated mask slot.
a SigSet
, or a p-value vector if return.pval is TRUE
sset <- sesameDataGet("HM450.1.TCGA.PAAD")$sset sum(mask(sset)) sset_with_mask <- detectionPoobEcdf(sset) sum(mask(sset_with_mask)) sset <- sesameDataGet("HM450.1.TCGA.PAAD")$sset sum(mask(sset)) sset_with_mask <- pOOBAH(sset) sum(mask(sset_with_mask))