noob: Noob background subtraction

In zwdzwd/sesame: SEnsible Step-wise Analysis of DNA MEthylation BeadChips

Noob background subtraction

Description

The function takes a SigDF and returns a modified SigDF with background subtracted. Background was modelled in a normal distribution and true signal in an exponential distribution. The Norm-Exp deconvolution is parameterized using Out-Of-Band (oob) probes. For species-specific processing, one should call inferSpecies on SigDF first. Multi-mapping probes are excluded.

Usage

noob(sdf, combine.neg = TRUE, offset = 15)

Arguments

sdf	a SigDF
combine.neg	whether to combine negative control probe.
offset	offset

Details

When combine.neg = TRUE, background will be parameterized by both negative control and out-of-band probes.

Value

a new SigDF with noob background correction

Examples

sdf <- sesameDataGet('EPIC.1.SigDF')
sdf.nb <- noob(sdf)

zwdzwd/sesame documentation built on Nov. 11, 2024, 9:33 a.m.