gds_idat2rg: Get IDATs as an RGChannelSet from GEO/GDS

In recountmethylation: Access and Analyze DNA Methylation Array Databases

Description

Queries and downloads GSM IDAT files in GEO Data Sets db, then returns the assay data as an "RGChannelSet", calling gds_idatquery() then minfi::read.metharray().

Usage

gds_idat2rg(
  gsmvi,
  rmdl = TRUE,
  ext = "gz",
  dfp = "./idats/",
  burl = paste0("ftp://ftp.ncbi.nlm.nih.gov/", "geo/samples/"),
  silent = TRUE
)

Arguments

gsmvi	A vector of GSM IDs (alphanumeric character strings).
rmdl	Whether to remove downloaded IDAT files when finished (default TRUE).
ext	Extension for downloaded files (default "gz").
dfp	Destination for IDAT downloads.
burl	Base URL string for the IDAT query (default "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/").
silent	Whether to suppress warnings on download removal (default TRUE).

Value

An RGChannelSet object

See Also

gds_idatquery(), read.metharray()

Examples

gsmvi <- c("GSM2465267", "GSM2814572")
fpath <- file.path(tempdir(), "gds_idat2rg_example")
rg <- gds_idat2rg(gsmvi, dfp = fpath)

recountmethylation documentation built on Nov. 8, 2020, 4:59 p.m.