readIDATpair: Import a pair of IDATs from one sample

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

Import a pair of IDATs from one sample

Description

The function takes a prefix string that are shared with _Grn.idat and _Red.idat. The function returns a SigDF.

Usage

readIDATpair(
  prefix.path,
  manifest = NULL,
  platform = "",
  min_beads = NULL,
  controls = NULL,
  verbose = FALSE
)

Arguments

prefix.path	sample prefix without _Grn.idat and _Red.idat
manifest	optional design manifest file
platform	EPIC, HM450 and HM27 etc.
min_beads	minimum bead number, probes with R or G smaller than this threshold will be masked. If NULL, no filtering based on bead count will be applied.
controls	optional control probe manifest file
verbose	be verbose? (FALSE)

Value

a SigDF

Examples

sdf <- readIDATpair(sub('_Grn.idat','',system.file(
    "extdata", "4207113116_A_Grn.idat", package = "sesameData")))

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