archs4_sample_info: Retrieves information for samples by GSE series or sample IDs
In denalitherapeutics/archs4: Wrappers to query and extract ARCHS4 data

Description Usage Arguments Value Examples

Fetch a tibble of series and sample information by querying the arcsh4 dataset by GEO sample (GSE) or sample (GSM) ids.

For each unique GEO series identifier ("GSEnnnn"), we will check if the ARCHS4 dataset is missing any of its samples when check_missing_samples is set to TRUE (default).

sample_info(x, id, columns = c("Sample_title", "Sample_source_name_ch1"),
  check_missing_samples = TRUE, ...)

archs4_sample_info(id, columns = c("Sample_title",
  "Sample_source_name_ch1"), sample_table = archs4_sample_table(datadir =
  datadir), sample_covariates = archs4_sample_covariates(datadir),
  check_missing_samples = TRUE, datadir = getOption("archs4.datadir"),
  ...)

`x`	an `Archs4Repository`
`id`	a character vector of GEO series or sample ids.
`columns`	the names of the sample metadata columns desired. This defaults to `c("Sample_title", "Sample_source_name_ch1")`. The values in `columns` must be a subset of the values enumerated in `archs4_sample_covariates()`.
`check_missing_samples`	When `TRUE` (the default), this function will check every unique GEO series identifier (`"GSEnnnn"`) for missing samples by using an NCBI Rest service via a call to `archs4_series_status()`, and `lookup_gse()`.
`sample_table`	the output from `archs4_sample_table()`, which lists the series_id,sample_id combinations found in the ARCHS4 repository.
`sample_covariates`	the `data.frame`-definition of the sample covariates found in the ARCHS4 datasetes, which is constructed via a call to `archs4_sample_covariates()`. The parameter is included in here so that a cached version of this `data.frame` can be re-used.
`datadir`	the directory that holds the archs4 data

a tibble of series_id, sample_id, sample_h5idx, sample_title, and sample_name columns. If the query sample or series query can't be found, then there will be an NA value for these columns. The query_type column will indicat whether the row was returned from querying by series or by sample.