gds_idatquery {recountmethylation} | R Documentation

## Query and download IDATs from GEO Data Sets

### Description

Queries GEO Data Sets for IDATs, and downloads available IDATs. This uses anticipated string pattern to construct the URL path for the query. IDATs are detected from the supplement for a GSE record.

### Usage

    gds_idatquery(
      gsmvi,
      ext = "gz",
      expand = TRUE,
      verbose = FALSE,
      dfp = "idats",
      burl = paste0("ftp://ftp.ncbi.nlm.nih.gov/geo/samples/")
    )

### Arguments

`gsmvi` | Vector of valid GSM IDs.
`ext` | Filename extension.
`expand` | Whether to expand compressed files.
`verbose` | Whether to show verbose messages (default FALSE).
`dfp` | Destination directory for downloads.
`burl` | Base URL string for RCurl query.

### Value

Lists the basename paths and filenames of IDATs downloaded.

### Examples

    gsmvi <- c("GSM2465267", "GSM2814572")
    gds_idatquery(gsmvi, dfp = file.path(tempdir(), "gds_idatquery_example"))

[Package recountmethylation version 1.0.0 Index]