geo_info {recount} | R Documentation

## Extract information from GEO for a given sample

### Description

This function uses GEOquery to extract information for a given sample. The GEO accession ids for the sample can be found in the study phenotype table.

### Usage

    geo_info(
      geoid,
      verbose = FALSE,
      sleep = 1/2,
      getGPL = FALSE,
      destdir = tempdir(),
      ...
    )

### Arguments

`geoid` | A character vector of length 1 with the GEO accession id for a given sample.
`verbose` | If `TRUE` the `geoid` will be shown.
`sleep` | The number of seconds (or fraction) to wait before downloading data using getGEO. This is important if you are looking over `geo_info()` given the constraints published at https://www.ncbi.nlm.nih.gov/books/NBK25497/.
`getGPL` | This argument is passed to getGEO and is set to `FALSE` by default to speed up the process.
`destdir` | This argument is passed to getGEO.
`...` | Additional arguments passed to getGEO.

### Value

Returns a DataFrame-class with the information from GEO available for the given sample.

### Author(s)

Leonardo Collado-Torres, Andrew Jaffe

### Examples

    geo_info("GSM836270")

[Package recount version 1.14.0 Index]