gds_idatquery: Query and download IDATs from GEO Data Sets

In recountmethylation: Access and Analyze DNA Methylation Array Databases

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"))

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