Retrieve the samples of a dataset
get_dataset_samples(
dataset,
useProcessedQuantitationType = TRUE,
quantitationType = NA_character_,
raw = getOption("gemma.raw", FALSE),
memoised = getOption("gemma.memoised", FALSE),
file = getOption("gemma.file", NA_character_),
overwrite = getOption("gemma.overwrite", FALSE)
)A numerical dataset identifier or a dataset short name
If TRUE, returns the samples according to the processed quantitation type. This is set to TRUE by default to ensure output of this function always matches with get_dataset_processed_expression, otherwise for single cell experiments in particular, the output will not include cell types.
If provided, returns the samples based on a given quantitation type. Using useProcessedQuantitationType instead should cover most use cases.
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.
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.
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.
Whether or not to overwrite if a file exists at the specified filename.
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
head(get_dataset_samples("GSE2018"))
#> sample.name sample.ID
#> <char> <int>
#> 1: BAL_47c_A0B1 1
#> 2: BAL_47b_A0B1 2
#> 3: BAL_47a_A0B0 3
#> 4: BAL_46_A2B0 4
#> 5: BAL_45b_A2B0 5
#> 6: BAL_45a_A1B0 6
#> sample.description
#> <char>
#> 1: Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=0 and B=1 (Non-acute rejection). One of three samples from the same patient, different visits.\nSource GEO sample is GSM36456\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=1 (Non-acute rejection). One of three samples from the same patient, different visits.\nSource GEO sample is GSM36455\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). One of three samples from the same patient, different visits.\nSource GEO sample is GSM36454\nLast updated (according to GEO): May 27 2005
#> 4: Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=2 and B=0 (Acute rejection).\nSource GEO sample is GSM36453\nLast updated (according to GEO): May 27 2005
#> 5: Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=2 and B=0 (Acute rejection). One of two samples from the same patient, different visits\nSource GEO sample is GSM36452\nLast updated (according to GEO): May 27 2005
#> 6: Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=1 and B=0 (Non-acute rejection). One of two samples from the same patient, different visits.\nSource GEO sample is GSM36451\nLast updated (according to GEO): May 27 2005
#> sample.outlier sample.accession sample.database sample.characteristics
#> <lgcl> <char> <char> <list>
#> 1: FALSE GSM36456 GEO c("BioSo....
#> 2: FALSE GSM36455 GEO c("BioSo....
#> 3: FALSE GSM36454 GEO c("BioSo....
#> 4: FALSE GSM36453 GEO c("BioSo....
#> 5: FALSE GSM36452 GEO c("BioSo....
#> 6: FALSE GSM36451 GEO c("BioSo....
#> sample.factorValues
#> <list>
#> 1: c("block....
#> 2: c("block....
#> 3: c("block....
#> 4: c("disea....
#> 5: c("block....
#> 6: c("block....
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