gds_idat2rg {recountmethylation} | R Documentation

## Get IDATs as an RGChannelSet from GEO/GDS

### 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 <- try(gds_idat2rg(gsmvi, dfp = fpath))

[Package recountmethylation version 1.2.3 Index]