Extract information from GEO for a given sample

Source: R/geo_info.R

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.

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

Leonardo Collado-Torres, Andrew Jaffe

Examples

geo_info("GSM836270")
#> Using locally cached version of GSM836270 found here:
#> /tmp/RtmpJLggZ6/GSM836270.soft 
#> DataFrame with 1 row and 25 columns
#>   channel_count data_row_count            description geo_accession
#>     <character>    <character>            <character>   <character>
#> 1             1              0 Uninduced K562-shSRF..     GSM836270
#>      growth_protocol_ch1       instrument_model last_update_date molecule_ch1
#>              <character>            <character>      <character>  <character>
#> 1 Refer to http://huds.. Illumina Genome Anal..      May 15 2019    total RNA
#>   organism_ch1 platform_id source_name_ch1                status
#>    <character> <character>     <character>           <character>
#> 1 Homo sapiens    GPL10999          SL2933 Public on Dec 01 2011
#>   submission_date   taxid_ch1                  title treatment_protocol_ch1
#>       <character> <character>            <character>            <character>
#> 1     Nov 18 2011        9606 K562 cells with shRN.. Refer to http://huds..
#>          type                                       characteristics
#>   <character>                                       <CharacterList>
#> 1         SRA cells: K562,shRNA expression: no,treatment: Puromycin
#>     data_processing                           contact                extract
#>     <CharacterList>                   <CharacterList>        <CharacterList>
#> 1 Bowtie, Cufflinks 601 Genome Way,Huntsville,USA,... Standard Illumina RN..
#>                       library
#>               <CharacterList>
#> 1 cDNA,transcriptomic,RNA-Seq
#>                                                               relation
#>                                                        <CharacterList>
#> 1 SRA: https://www.ncb..,BioSample: https://w..,Named Annotation: NA..
#>            series
#>   <CharacterList>
#> 1        GSE33816
#>                                                     supplementary_file
#>                                                        <CharacterList>
#> 1 ftp://ftp.ncbi.nlm.n..,ftp://ftp.ncbi.nlm.n..,ftp://ftp.ncbi.nlm.n..