detectionPoobEcdf {sesame}R Documentation

Detection P-value based on ECDF of out-of-band signal

Description

aka pOOBAH (p-vals by Out-Of-Band Array Hybridization)

Usage

detectionPoobEcdf(sset, return.pval = FALSE, pval.threshold = 0.05)

pOOBAH(sset, return.pval = FALSE, pval.threshold = 0.05)

Arguments

sset

a SigSet

return.pval

whether to return p-values, instead of a masked SigSet

pval.threshold

minimum p-value to mask

Details

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.

Value

a SigSet, or a p-value vector if return.pval is TRUE

Examples

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))

[Package sesame version 1.10.5 Index]