detectionPnegNormGS {sesame}R Documentation

Detection P-value emulating Genome Studio

Description

The function takes a SigSet as input, computes detection p-value using negative control probes parametrized in a normal distribution a la Genome Studio and returns a new SigSet with an updated mask slot.

Usage

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

Arguments

sset

a SigSet

pval.threshold

minimum p-value to mask

return.pval

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

Details

P-value is calculated using negative control probes as the estimate of background where Grn channel and Red channel are merged. But when estimating p-value the Red and Grn are summed (non-ideal).

Value

detection p-value

Examples

sset <- sesameDataGet("HM450.1.TCGA.PAAD")$sset
sum(mask(sset))
sset_with_mask <- detectionPnegNormGS(sset)
sum(mask(sset_with_mask))

[Package sesame version 1.10.5 Index]