Extract Sample Metadata from GEO.

Usage

ExtractGEOMeta(
  acce,
  platform = NULL,
  down.supp = FALSE,
  supp.idx = 1,
  timeout = 3600,
  ...
)

Arguments

acce: GEO accession number.
platform: Platform information/field. Default: NULL (all platforms).
down.supp: Logical value, whether to download supplementary files to extract sample metadata. If TRUE, always download supplementary files. If FALSE, extract GEO sample metadata. Default: FALSE.
supp.idx: The index of supplementary files to download. Default: 1.
timeout: Timeout for download.file. Default: 3600.
...: Parameters for getGEO.

Value

Dataframe contains all metadata of provided GEO accession number.

Examples

# \donttest{
# users may need to set the size of the connection buffer
# Sys.setenv("VROOM_CONNECTION_SIZE" = 131072 * 60)
# extract GEO sample metadata of specified platform
GSE200257.meta <- ExtractGEOMeta(acce = "GSE200257", platform = "GPL24676")
# extract sample metadata from supplementary files
GSE292261.meta.supp <- ExtractGEOMetaSupp(acce = "GSE292261", supp.idx = 4)
# }