processFromIDATs: read in a directory's worth of IDATs, QC them, optionally...

In ttriche/sesamizeGEO: the poor man's methylation suite (cf. `sesamizer`)

read in a directory's worth of IDATs, QC them, optionally sesamize them all

Description

Note: this function simply reads all IDATs in the current directory, runs QC, stuffs in metadata, and (if !justRgSet) sesamizes it.

Usage

processFromIDATs(
  frags = 1:3,
  targets = NULL,
  addgeo = FALSE,
  justRgSet = FALSE,
  forSesame = FALSE,
  verbose = FALSE,
  ...
)

Arguments

frags	which elements of the filenames are relevant? (1:3)
targets	a targets dataframe (will be passed to minfi for reading)
addgeo	optional: try to annotate from GEO? (FALSE)
justRgSet	optional: dump the result and don't sesamize? (FALSE)
forSesame	optional: avoid loading minfi data structures? (FALSE)
...	options to pass to sesamize

Details

minfi is becoming a pain in the ass to deal with due to its dependencies, so this function can emit various SummarizedExperiment-derived results (whether an RGChannelSet, a GenomicRatioSet, a SummarizedExperiment, or a SingleCellExperiment, depending upon its parameters). The only real guarantee is that, in the absence of an error, a SummarizedExperiment-derived object will be returned, and it will accommodate the usual generic getWhatever()s.

Value

a SummarizedExperiment-derived object of some sort (see Details)

ttriche/sesamizeGEO documentation built on Nov. 12, 2023, 5:42 p.m.