getDEE2: getDEE2: Programmatic access to the DEE2 RNA expression...

In markziemann/getDEE2: Programmatic access to the DEE2 RNA expression dataset

Description

Digital Expression Explorer 2 (or DEE2 for short) is a repository of processed RNA-seq data in the form of counts. It was designed so that researchers could undertake re-analysis and meta-analysis of published RNA-seq studies quickly and easily. This package provides an R interface to access these expression data. More information about the DEE2 project can be found at the project homepage (http://dee2.io) and main publication (https://doi.org/10.1093/gigascience/giz022).

The getDEE2 function fetches gene expression data from the DEE2 database of RNA sequencing data and returns it as a SummarizedExperiment object.

Usage

getDEE2(
  species,
  SRRvec,
  counts = "GeneCounts",
  metadata = NULL,
  outfile = NULL,
  legacy = FALSE,
  baseURL = "http://dee2.io/cgi-bin/request.sh?",
  ...
)

Arguments

species	A character string matching the species of interest.
SRRvec	A character string or vector of SRA run accession numbers.
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.
metadata	(Optional) name of R object for the meta data. Providing the metadata will speed up performance if multiple queries are made in a session. If left blank, the metadata will be fetched once again.
outfile	An optional file name for the downloaded dataset.
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

# Example workflow
# Fetch metadata
mdat <- getDEE2Metadata("celegans")
# filter metadata for SRA project SRP009256
mdat1 <- mdat[which(mdat$SRP_accession %in% "SRP009256"),]
# create a vector of SRA run accessions to fetch
SRRvec <- as.vector(mdat1$SRR_accession)
# obtain the data as a SummarizedExperiment
x <- getDEE2("celegans",SRRvec,metadata=mdat,counts="GeneCounts")
# Next, downstream analysis with your favourite Bioconductor tools :)
x<-getDEE2("ecoli",c("SRR1613487","SRR1613488"))

markziemann/getDEE2 documentation built on Dec. 21, 2021, 2:48 p.m.