fetch

This function uses the NCBI SRA Toolkit via <code><a href="/link/system2()?package=seeker&version=1.1.6" data-mini-rdoc="seeker::system2()">system2()</a></code> to download files
from SRA and convert them to fastq.gz. To process files in parallel, register
a parallel backend, e.g., using <code>doParallel::registerDoParallel()</code>. Beware
that intermediate files created by fasterq-dump are uncompressed and could
require hundreds of gigabytes if files are processed in parallel.

Wrapper around various existing tools and command-line interfaces,
providing a standard interface, simple parallelization, and detailed logging.
For microarray data, maps probe sets to standard gene IDs, building on
'GEOquery' Davis and Meltzer (2007) <doi:10.1093/bioinformatics/btm254>,
'ArrayExpress' Kauffmann et al. (2009) <doi:10.1093/bioinformatics/btp354>,
Robust multi-array average 'RMA' Irizarry et al. (2003) <doi:10.1093/biostatistics/4.2.249>,
and 'BrainArray' Dai et al. (2005) <doi:10.1093/nar/gni179>.
For RNA-seq data, fetches metadata and raw reads from National Center for Biotechnology
Information (NCBI) Sequence Read Archive (SRA), performs standard adapter and
quality trimming using 'TrimGalore' Krueger <https://github.com/FelixKrueger/TrimGalore>,
performs quality control checks using 'FastQC' Andrews <https://github.com/s-andrews/FastQC>,
quantifies transcript abundances using 'salmon' Patro et al. (2017) <doi:10.1038/nmeth.4197> and potentially
'refgenie' Stolarczyk et al. (2020) <doi:10.1093/gigascience/giz149>,
aggregates the results using 'MultiQC' Ewels et al. (2016) <doi:10.1093/bioinformatics/btw354>,
maps transcripts to genes using 'biomaRt' Durinkck et al. (2009) <doi:10.1038/nprot.2009.97>,
and summarizes transcript-level quantifications for gene-level analyses using
'tximport' Soneson et al. (2015) <doi:10.12688/f1000research.7563.2>.

Jake Hughey

seeker

Simplified Fetching and Processing of Microarray and RNA-Seq
Data

Josh Schoenbachler

fetch function

<dl><dt>accessions</dt>
<dd>Character vector of SRA run accessions.</dd>
<dt>outputDir</dt>
<dd>String indicating the local directory in which to save the
files. Will be created if it doesn't exist.</dd>
<dt>overwrite</dt>
<dd>Logical indicating whether to overwrite files that already
exist in <code>outputDir</code>.</dd>
<dt>keepSra</dt>
<dd>Logical indicating whether to keep the ".sra" files.</dd>
<dt>prefetchCmd</dt>
<dd>String indicating command for prefetch, which downloads
".sra" files.</dd>
<dt>prefetchArgs</dt>
<dd>Character vector indicating arguments to pass to
prefetch.</dd>
<dt>fasterqdumpCmd</dt>
<dd>String indicating command for fasterq-dump, which
uses ".sra" files to create ".fastq" files.</dd>
<dt>fasterqdumpArgs</dt>
<dd>Character vector indicating arguments to pass to
fasterq-dump.</dd>
<dt>pigzCmd</dt>
<dd>String indicating command for pigz, which converts ".fastq"
files to ".fastq.gz" files.</dd>
<dt>pigzArgs</dt>
<dd>Character vector indicating arguments to pass to pigz.</dd></dl>

Arguments

This function uses the NCBI SRA Toolkit via <code><a href='https://rdrr.io/r/base/system2.html'>system2()</a></code> to download files
from SRA and convert them to fastq.gz. To process files in parallel, register
a parallel backend, e.g., using <code>doParallel::registerDoParallel()</code>. Beware
that intermediate files created by fasterq-dump are uncompressed and could
require hundreds of gigabytes if files are processed in parallel.

Fetch files — fetch

<dl>

<dt>accessions</dt>
<dd>Character vector of SRA run accessions.</dd>


<dt>outputDir</dt>
<dd>String indicating the local directory in which to save the
files. Will be created if it doesn't exist.</dd>


<dt>overwrite</dt>
<dd>Logical indicating whether to overwrite files that already
exist in <code>outputDir</code>.</dd>


<dt>keepSra</dt>
<dd>Logical indicating whether to keep the ".sra" files.</dd>


<dt>prefetchCmd</dt>
<dd>String indicating command for prefetch, which downloads
".sra" files.</dd>


<dt>prefetchArgs</dt>
<dd>Character vector indicating arguments to pass to
prefetch.</dd>


<dt>fasterqdumpCmd</dt>
<dd>String indicating command for fasterq-dump, which
uses ".sra" files to create ".fastq" files.</dd>


<dt>fasterqdumpArgs</dt>
<dd>Character vector indicating arguments to pass to
fasterq-dump.</dd>


<dt>pigzCmd</dt>
<dd>String indicating command for pigz, which converts ".fastq"
files to ".fastq.gz" files.</dd>


<dt>pigzArgs</dt>
<dd>Character vector indicating arguments to pass to pigz.</dd>

</dl>

fetch: Fetch files

Description

Usage

Value

Arguments

See Also