bisConversionControl: Compute internal bisulfite conversion control

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

Compute internal bisulfite conversion control

Description

Compute GCT score for internal bisulfite conversion control. The function takes a SigSet as input. The higher the GCT score, the more likely the incomplete conversion.

Usage

bisConversionControl(sdf, extR = NULL, extA = NULL, verbose = FALSE)

Arguments

sdf	a SigDF
extR	a vector of probe IDs for Infinium-I probes that extend to converted A
extA	a vector of probe IDs for Infinium-I probes that extend to original A
verbose	print more messages

Value

GCT score (the higher, the more incomplete conversion)

Examples

sesameDataCache() # if not done yet
sdf <- sesameDataGet('EPIC.1.SigDF')
bisConversionControl(sdf)

## For more recent platforms like EPICv2, MSA:
## One need extR and extA of other arrays using the sesameAnno
## Not run: 
mft = sesameAnno_buildManifestGRanges(sprintf(
  "%s/EPICv2/EPICv2.hg38.manifest.tsv.gz",
  "https://github.com/zhou-lab/InfiniumAnnotationV1/raw/main/Anno/"),
  columns="nextBase")
extR = names(mft)[!is.na(mft$nextBase) & mft$nextBase=="R"]
extA = names(mft)[!is.na(mft$nextBase) & mft$nextBase=="A"]

## End(Not run)

zwdzwd/sesame documentation built on Dec. 21, 2024, 1:20 p.m.