Retrieve Series Matrix and Create ExpressionSet

The function downloads and parses the relevant Series Matrix files, optionally mapping platform IDs to Bioconductor annotation packages.

Usage

geo_matrix(
  accession,
  add_gpl = NULL,
  pdata_from_soft = FALSE,
  ftp_over_https = NULL,
  handle_opts = list(),
  odir = getwd()
)

Arguments

accession

A character of GEO accession IDs. Examples:

• DataSets (GDS): "GDS505", "GDS606", "GDS1234", "GDS9999", etc.

• Series (GSE): "GSE2", "GSE22", "GSE100", "GSE2000", etc.

• Platforms (GPL): "GPL96", "GPL570", "GPL10558", etc.

• Samples (GSM): "GSM12345", "GSM67890", "GSM112233", etc.

add_gpl

Logical or NULL. Whether to include platform information (the featureData slot). If NULL (default), the function attempts to map the GPL accession to a Bioconductor annotation package. If successful, the annotation slot is updated and add_gpl is set to FALSE; otherwise, add_gpl is set to TRUE.

pdata_from_soft

Logical. Specifies whether to derive phenoData from the GSE series SOFT file. Defaults to FALSE, in which case phenoData is parsed directly from the series matrix file. Set to TRUE if you encounter issues parsing characteristics_ch* columns correctly, as it will attempt to retrieve the data from the SOFT file instead.

ftp_over_https

Logical scalar. If TRUE, connects to GEO FTP server via HTTPS (https://ftp.ncbi.nlm.nih.gov/geo); otherwise uses plain FTP (ftp://ftp.ncbi.nlm.nih.gov/geo). Only applicable to GEO FTP server access.

handle_opts

A list of named options / headers to be set in the multi_download.

odir

Destination directory for downloads. Defaults to the current working directory.

Value

An ExpressionSet or a list of ExpressionSets, one per Series Matrix file.

Examples

# \donttest{
if (require("Biobase")) {
    eset <- geo_matrix("GSE10", odir = tempdir())
}
#> Loading required package: Biobase
#> Loading required package: BiocGenerics
#> Loading required package: generics
#> 
#> Attaching package: ‘generics’
#> The following objects are masked from ‘package:base’:
#> 
#>     as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
#>     setequal, union
#> 
#> Attaching package: ‘BiocGenerics’
#> The following objects are masked from ‘package:stats’:
#> 
#>     IQR, mad, sd, var, xtabs
#> The following objects are masked from ‘package:base’:
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
#>     as.data.frame, basename, cbind, colnames, dirname, do.call,
#>     duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
#>     mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
#>     rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
#>     unsplit, which.max, which.min
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> Downloading 1 file
#> ℹ No Bioconductor annotation package available for platform "GPL4".
#> Downloading 1 file
#> ℹ annot file in FTP site for "GPL4" is not available, will use data amount file from GEO Accession Site instead
#> Downloading 1 file
#> ✔ Parsing 1 Series matrix successfully!
# }