detectionPfixedNorm {sesame}R Documentation

Detection P-value based on normal fitting with gived parameters

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

detectionPfixedNorm(
  sset,
  muG = 500,
  sdG = 200,
  muR = 500,
  sdR = 200,
  pval.threshold = 0.05,
  return.pval = FALSE
)

Arguments

sset

a SigSet

muG

mean of background in Grn channel

sdG

SD of background in Grn channel

muR

mean of background in Red channel

sdR

SD of background in Red channel

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 a fixed normal distribution. p-value is taken from the minimum of the p-value of the two alleles (color depends on probe design).

Value

detection p-value

Examples

sset <- sesameDataGet('HM450.1.TCGA.PAAD')$sset
sum(mask(sset))
sset_with_mask <- detectionPfixedNorm(sset)
sum(mask(sset_with_mask))


[Package sesame version 1.10.5 Index]