detectionPnegNormTotal {sesame}

R Documentation

Detection P-value based on normal fitting the negative controls, channels are first summed

Description

The function takes a SigSet as input, computes detection p-value using negative control probes parametrized in a normal distribution with the two channels summed first and returns a new SigSet with an updated mask slot. The SD is summed to emulate the SD of the summed signal (not the most accurate treatment).

Usage

detectionPnegNormTotal(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

Value

detection p-value

Examples

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

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