archs4_sample_table: Lists the GEO series and samples available in the human and...
In denalitherapeutics/archs4: Wrappers to query and extract ARCHS4 data

Description Usage Arguments Details Value

This function queries the human and mouse gene expression matrices from the ARCHS4 data release and combines their GEO series and sample identifiers into a long table, annotated with the organism the samples come from.

sample_table(x, ...)

archs4_sample_table(feature_type = c("all", "gene", "transcript"),
  unroll_series = TRUE, datadir = getOption("archs4.datadir"))

`x`	an `Archs4Repository`
`feature_type`	currently, the `"gene"` and `"transcript"` datasets are not the same.
`unroll_series`	There are some malformed series identifiers, like `"GSE36025Xx-xXGSE49417Xx-xXGSE49847"` when the same sample_id appears in multiple series. When this is `TRUE` (default), the series_id's are unrolled and cleaned up.
`datadir`	the directory that holds the archs4 data

This function executes very quickly (less thatn 0.10th of a second), so most sample-level query functions in this package which you would think would benefit from specifying human/mouse don't have to, as they will join into this table to find out what species is being queried.

a tibble of series_id, sample_id, species columns

denalitherapeutics/archs4 documentation built on May 17, 2019, 1:29 p.m.