geo_info: Extract information from GEO for a given sample

Description Usage Arguments Value Author(s) Examples

View source: R/geo_info.R

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

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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

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geo_info("GSM836270")

recount documentation built on Dec. 20, 2020, 2:01 a.m.