archs4_series_status: Checks which samples from a single series are present/absent.

In denalitherapeutics/archs4: Wrappers to query and extract ARCHS4 data

Description

Due to download or alignment issues, the ARCHS4 data processing pipeline may not include all of the samples included in a particular GEO series. This function will return a table with an in_archs4 columns that indicates whether or not a sample from a particular series is present in ARCHS4.

Usage

series_status(x, id, ...)

archs4_series_status(id, sample_table = archs4_sample_table(datadir =
  datadir), datadir = getOption("archs4.datadir"), ...)

Arguments

x	an Archs4Repository
id	a single GEO series id, ie. "GSEnnnnn"
sample_table	the output from archs4_sample_table(), which lists the series_id,sample_id combinations found in the ARCHS4 repository.
datadir	the directory that holds the archs4 data

Value

a tibble of information for a series.

Examples

info <- archs4_series_status("GSE89189")

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