Package 'getDEE2'

Title: 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. As of April 2020, over 1 million SRA datasets have been processed. 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).
Authors: Mark Ziemann [aut, cre], Antony Kaspi [aut]
Maintainer: Mark Ziemann <[email protected]>
License: GPL-3
Version: 1.15.0
Built: 2024-10-02 05:14:46 UTC
Source: https://github.com/bioc/getDEE2

Help Index

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"))

Get a DEE2 project bundle

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")

Get DEE2 Metadata

Description

This function fetches the short metadata for the species of interest.

Usage

getDEE2Metadata(species, outfile = NULL, ...)

Arguments

species

A character string matching a species of interest.
outfile

Optional filename.
...

Additional parameters to be passed to download.file.

Value

a table of metadata.

Examples

ecoli_metadata <- getDEE2Metadata("ecoli")

Get a table of all completed projects at DEE2

Description

This function fetches a table listing all completed projects that are available at DEE2

Usage

list_bundles(species)

Arguments

species

A character string matching a species of interest.

Value

a table of project bundles available at DEE2.io/huge

Examples

bundles <- list_bundles("celegans")

Load Full Metadata

Description

This function loads the full metadata, which contains many fields.

Usage

loadFullMeta(zipname)

Arguments

zipname

Path to the zipfile.

Value

a dataframe of full metadata.

Examples

x <- getDEE2("ecoli",c("SRR1613487","SRR1613488"),outfile="mydata.zip")
y <- loadFullMeta("mydata.zip")

Load Gene Counts

Description

This function loads STAR gene level counts from a downloaded zip file.

Usage

loadGeneCounts(zipname)

Arguments

zipname

Path to the zipfile.

Value

a dataframe of gene expression counts.

Examples

x <- getDEE2("ecoli",c("SRR1613487","SRR1613488"),outfile="mydata.zip")
y <- loadGeneCounts("mydata.zip")

Load Gene Info

Description

This function loads gene information. This information includes gene names and lengths which is useful for downstream analysis.

Usage

loadGeneInfo(zipname)

Arguments

zipname

Path to the zipfile.

Value

a dataframe of gene information.

Examples

x <- getDEE2("ecoli",c("SRR1613487","SRR1613488"),outfile="mydata.zip")
y <- loadGeneInfo("mydata.zip")

Load Quality Control Info

Description

This function loads quality control data. More information about the QC metrics is available from the project github page: https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md

Usage

loadQcMx(zipname)

Arguments

zipname

Path to the zipfile.

Value

a dataframe of quality control metrics.

Examples

x <- getDEE2("ecoli",c("SRR1613487","SRR1613488"),outfile="mydata.zip")
y <- loadQcMx("mydata.zip")

Load Summary Metadata

Description

This function loads the summary metadata, which are the most relevant SRA accession numbers.

Usage

loadSummaryMeta(zipname)

Arguments

zipname

Path to the zipfile.

Value

a dataframe of summary metadata.

Examples

x <- getDEE2("ecoli",c("SRR1613487","SRR1613488"),outfile="mydata.zip")
y <- loadSummaryMeta("mydata.zip")

Load Transcript Counts

Description

This function loads Kallisto transcript level counts from a downloaded zip file.

Usage

loadTxCounts(zipname)

Arguments

zipname

Path to the zipfile.

Value

a dataframe of transcript expression counts.

Examples

x <- getDEE2("ecoli",c("SRR1613487","SRR1613488"),outfile="mydata.zip")
y <- loadTxCounts("mydata.zip")

Load Transcript Info

Description

This function loads transcript information. This information includes transcript lengths, corresponding parent gene accession and gene symbol that might be useful for downstream analysis.

Usage

loadTxInfo(zipname)

Arguments

zipname

Path to the zipfile.

Value

a dataframe of transcript info

Examples

x <- getDEE2("ecoli",c("SRR1613487","SRR1613488"),outfile="mydata.zip")
y <- loadTxInfo("mydata.zip")

Query whether a project bundle is available from DEE2

Description

This function sends a query to check whether a dataset is available or not.

Usage

query_bundles(species, query, col, bundles = NULL)

Arguments

species

A character string matching a 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.
bundles

optional table of previously downloaded bundles.

Value

a list of datasets that are present and absent.

Examples

query_bundles("celegans", c("SRP133403","SRP133439"), col = "SRP_accession")

Query Whether a DEE2 Dataset is Available

Description

This function sends a query to check whether a dataset is available or not.

Usage

queryDEE2(species, SRRvec, metadata = NULL, ...)

Arguments

species

A character string matching a species of interest.
SRRvec

A character string or vector thereof of SRA run accession numbers.
metadata

optional R object of DEE2 metadata to query.
...

Additional parameters to be passed to download.file.

Value

a list of datasets that are present and absent.

Examples

x <- queryDEE2("ecoli",c("SRR1067773","SRR5350513"))

Create summarizedExperiment object

Description

This function creates a SummarizedExperiment object from a legacy getDEE2 dataset

Usage

se(x, counts = "GeneCounts")

Arguments

x

a getDEE2 object.
counts

select "GeneCounts" for STAR based gene counts, "TxCounts" for kallisto transcript level counts or "Tx2Gene" for transcript counts aggregated to gene level. Default is "GeneCounts"

Value

a SummarizedExperiment object

Examples

x <- getDEE2("ecoli",c("SRR1613487","SRR1613488"),legacy=TRUE)
y <- se(x)

Summarized run data to experiments

Description

Sometimes, each SRA experiment data is represented in two or more runs and they need to be aggregated.

Usage

srx_agg(x, counts = "GeneCounts")

Arguments

x

a getDEE2 object.
counts

select "GeneCounts" for STAR based gene counts, "TxCounts" for kallisto transcript level counts or "Tx2Gene" for transcript counts aggregated to gene level. Default is "GeneCounts"

Value

a dataframe with gene expression data summarised to SRA experiment accession numbers rather than run accession numbers.

Examples

x <- getDEE2("ecoli",c("SRR1613487","SRR1613488"),legacy=TRUE)
y <- srx_agg(x)

Aggregate Transcript Counts to Gene-Level Counts

Description

This function converts Kallisto transcript-level expression estimates to gene-level estimates. Counts for each transcript are summed to get an aggregated gene level score.

Usage

Tx2Gene(x)

Arguments

x

a getDEE2 object.

Value

a dataframe of gene expression counts.

Examples

x <- getDEE2("scerevisiae",c("SRR1755149","SRR1755150"),legacy=TRUE)
x <- Tx2Gene(x)