detectionPnegNorm {sesame}

R Documentation

Detection P-value based on normal fitting the negative controls

Description

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

Usage

detectionPnegNorm(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

Background of Grn and Red are estimated separately from negative control probes-parameterized normal distribution. p-value is taken from the minimum of the p-value of the two alleles (color depends on probe design).

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 <- detectionPnegNorm(sset)
sum(mask(sset_with_mask))

---