Retrieve the samples of a dataset

get_dataset_samples(
  dataset,
  raw = getOption("gemma.raw", FALSE),
  memoised = getOption("gemma.memoised", FALSE),
  file = getOption("gemma.file", NA_character_),
  overwrite = getOption("gemma.overwrite", FALSE)
)

Arguments

dataset: A numerical dataset identifier or a dataset short name
raw: TRUE to receive results as-is from Gemma, or FALSE to enable parsing. Raw results usually contain additional fields and flags that are omitted in the parsed results.
memoised: Whether or not to save to cache for future calls with the same inputs and use the result saved in cache if a result is already saved. Doing options(gemma.memoised = TRUE) will ensure that the cache is always used. Use forget_gemma_memoised to clear the cache.
file: The name of a file to save the results to, or NULL to not write results to a file. If raw == TRUE, the output will be the raw endpoint from the API, likely a JSON or a gzip file. Otherwise, it will be a RDS file.
overwrite: Whether or not to overwrite if a file exists at the specified filename.

Value

A data table with information about the samples of the queried dataset. A list if raw = TRUE. A 404 error if the given identifier does not map to any object.

The fields of the output data.table are:

sample.name: Internal name given to the sample.
sample.ID: Internal ID of the sample
sample.description: Free text description of the sample
sample.outlier: Whether or not the sample is marked as an outlier
sample.accession: Accession ID of the sample in it's original database
sample.database: Database of origin for the sample
sample.characteristics: Characteristics of the sample. This field is a data table
sample.factorValues: Experimental factor values of the sample. This field is a data table

Examples

head(get_dataset_samples("GSE2018"))
#>     sample.name sample.ID
#>          <char>     <int>
#> 1:   BAL_1_A0B0        31
#> 2: BAL_27a_A0B0        20
#> 3:  BAL_43_A0B0         9
#> 4:  BAL_13_A0B0        29
#> 5:  BAL_29_A1B0        18
#> 6: BAL_44b_A0B0         7
#>                                                                                                                                                                                                                                       sample.description
#>                                                                                                                                                                                                                                                   <char>
#> 1:                                                             Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=0 and B=0 (Non-acute rejection).\nSource GEO sample is GSM36426\nLast updated (according to GEO): May 27 2005
#> 2:  Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=0 and B=0 (Non-acute rejection). One of two samples from the same patient, different visits\nSource GEO sample is GSM36437\nLast updated (according to GEO): May 27 2005
#> 3:                                                             Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=0 and B=0 (Non-acute rejection).\nSource GEO sample is GSM36448\nLast updated (according to GEO): May 27 2005
#> 4:                                                             Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=0 and B=0 (Non-acute rejection).\nSource GEO sample is GSM36428\nLast updated (according to GEO): May 27 2005
#> 5:                                                             Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=1 and B=0 (Non-acute rejection).\nSource GEO sample is GSM36439\nLast updated (according to GEO): May 27 2005
#> 6:  Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=0 and B=0 (Non-acute rejection). One of two samples from the same patient, different visits\nSource GEO sample is GSM36450\nLast updated (according to GEO): May 27 2005
#>    sample.outlier sample.accession sample.database sample.characteristics
#>            <lgcl>           <char>          <char>                 <list>
#> 1:          FALSE         GSM36426             GEO           c("molec....
#> 2:          FALSE         GSM36437             GEO           c("molec....
#> 3:          FALSE         GSM36448             GEO           c("molec....
#> 4:          FALSE         GSM36428             GEO           c("molec....
#> 5:          FALSE         GSM36439             GEO           c("molec....
#> 6:          FALSE         GSM36450             GEO           c("molec....
#>    sample.factorValues
#>                 <list>
#> 1:        c("block....
#> 2:        c("block....
#> 3:        c("block....
#> 4:        c("block....
#> 5:        c("block....
#> 6:        c("disea....