sesamiser: like getGEO, if getGEO worked directly on IDATs and masked...

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

like getGEO, if getGEO worked directly on IDATs and masked off deletions

Description

Note 0: this function will download the data with getGEO first (!) Note 1: you may fare better with recountmethylation, check there first. Note 2: this would work just as well off the moby recountmethylation rgset. Note 3: this function will exit with an error if no IDATs are available. Note 4: if there is one supplementary file column, we will need to split it.

Usage

sesamiser(
  GSE,
  element = 1,
  suppcols = c("supplementary_file", "supplementary_file.1"),
  path = ".",
  ...
)

Arguments

GSE	which GSE to get
element	which element of the getGEO result to work on? (1)
suppcols	cols ("supplementary_file", "supplementary_file.1")
...	additional arguments to pass to read.metharray()

Value

             a sesamized GenomicRatioSet

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