salmon

This function calls
<a href="https://combine-lab.github.io/salmon/">salmon</a>
using <code><a href="/link/system2()?package=seeker&version=1.1.6" data-mini-rdoc="seeker::system2()">system2()</a></code>. To run in parallel, register a parallel backend, e.g.,
using <code>doParallel::registerDoParallel()</code>.

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

salmon function

<dl><dt>filepaths</dt>
<dd>Paths to fastq files. For single-end reads, each element
should be a single filepath. For paired-end reads, each element should be
two filepaths separated by ";".</dd>
<dt>samples</dt>
<dd>Corresponding sample names for fastq files.</dd>
<dt>indexDir</dt>
<dd>Directory that contains salmon index.</dd>
<dt>outputDir</dt>
<dd>Directory in which to store output. Will be created if it
doesn't exist.</dd>
<dt>cmd</dt>
<dd>Name or path of the command-line interface.</dd>
<dt>args</dt>
<dd>Additional arguments to pass to the command-line interface.</dd>
<dt>compress</dt>
<dd>Logical indicating whether to gzip the quantification file
(quant.sf) from salmon. Does not affect downstream analysis.</dd></dl>

Arguments

This function calls
<a href='https://combine-lab.github.io/salmon/'>salmon</a>
using <code><a href='https://rdrr.io/r/base/system2.html'>system2()</a></code>. To run in parallel, register a parallel backend, e.g.,
using <code>doParallel::registerDoParallel()</code>.

Run Salmon — salmon

<dl>

<dt>filepaths</dt>
<dd>Paths to fastq files. For single-end reads, each element
should be a single filepath. For paired-end reads, each element should be
two filepaths separated by ";".</dd>


<dt>samples</dt>
<dd>Corresponding sample names for fastq files.</dd>


<dt>indexDir</dt>
<dd>Directory that contains salmon index.</dd>


<dt>outputDir</dt>
<dd>Directory in which to store output. Will be created if it
doesn't exist.</dd>


<dt>cmd</dt>
<dd>Name or path of the command-line interface.</dd>


<dt>args</dt>
<dd>Additional arguments to pass to the command-line interface.</dd>


<dt>compress</dt>
<dd>Logical indicating whether to gzip the quantification file
(quant.sf) from salmon. Does not affect downstream analysis.</dd>

</dl>

salmon: Run Salmon

Description

Usage

Value

Arguments

See Also