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))

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