getDEE2_bundle: Get a DEE2 project bundle

In getDEE2: Programmatic access to the DEE2 RNA expression dataset

Description

The getDEE2_bundle function fetches gene expression data from DEE2. This function will only work if all SRA runs have been successfully processed for an SRA project. This function returns a SummarizedExperiment object.

Usage

getDEE2_bundle(
  species,
  query,
  col,
  counts = "GeneCounts",
  bundles = NULL,
  legacy = FALSE,
  baseURL = "http://dee2.io/huge/",
  ...
)

Arguments

species	A character string matching the species of interest.
query	A character string, such as the SRA project accession number or the GEO series accession number
col	the column name to be queried, usually "SRP_accession" for SRA project accession or "GSE_accession" for GEO series accession.
counts	A string, either 'GeneCounts', 'TxCounts' or 'Tx2Gene'. When 'GeneCounts' is specified, STAR gene level counts are returned. When 'TxCounts' is specified, kallisto transcript counts are returned. When 'Tx2Gene' is specified, kallisto counts aggregated (by sum) on gene are returned. If left blank, "GeneCounts" will be fetched.
bundles	optional table of previously downloaded bundles. providing this will speed up performance if multiple queries are made in a session. If left blank, the bundle list will be fetched again.
legacy	Whether data should be returned in the legacy (list) format. Default is FALSE. Leave this FALSE if you want to receive data as Summarized experiment.
baseURL	The base URL of the service. Leave this as the default URL unless you want to download from a 3rd party mirror.
...	Additional parameters to be passed to download.file.

Value

a SummarizedExperiment object.

Examples

x <- getDEE2_bundle("celegans", "SRP133403",col="SRP_accession")

getDEE2 documentation built on Nov. 8, 2020, 7:46 p.m.