getTx2gene

This function uses the
<a href="https://doi.org/doi:10.18129/B9.bioc.biomaRt">biomaRt package</a>.

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

getTx2gene function

<dl><dt>organism</dt>
<dd>String used to pass <code>paste0(organism, "_gene_ensembl")</code> as the
<code>dataset</code> argument to <code>biomaRt::useEnsembl()</code>. To see available datasets,
do <code>mart = biomaRt::useEnsembl("genes"); biomaRt::listDatasets(mart)</code>.</dd>
<dt>version</dt>
<dd>Passed to <code>biomaRt::useEnsembl()</code>. <code>NULL</code> indicates the latest
version. To see available versions, do <code>biomaRt::listEnsemblArchives()</code>.</dd>
<dt>outputDir</dt>
<dd>Directory in which to save the result, a file named
"tx2gene.csv.gz". If <code>NULL</code>, no file is saved.</dd>
<dt>checkArgsOnly</dt>
<dd>Logical indicating whether to only check function
arguments. Used for testing.</dd></dl>

Arguments

This function uses the
<a href='https://doi.org/doi:10.18129/B9.bioc.biomaRt'>biomaRt package</a>.

Get mapping between transcripts and genes — getTx2gene

<dl>

<dt>organism</dt>
<dd>String used to pass <code>paste0(organism, "_gene_ensembl")</code> as the
<code>dataset</code> argument to <code>biomaRt::useEnsembl()</code>. To see available datasets,
do <code>mart = biomaRt::useEnsembl("genes"); biomaRt::listDatasets(mart)</code>.</dd>


<dt>version</dt>
<dd>Passed to <code>biomaRt::useEnsembl()</code>. <code>NULL</code> indicates the latest
version. To see available versions, do <code>biomaRt::listEnsemblArchives()</code>.</dd>


<dt>outputDir</dt>
<dd>Directory in which to save the result, a file named
"tx2gene.csv.gz". If <code>NULL</code>, no file is saved.</dd>


<dt>checkArgsOnly</dt>
<dd>Logical indicating whether to only check function
arguments. Used for testing.</dd>

</dl>

getTx2gene: Get mapping between transcripts and genes

Description

Usage

Value

Arguments

See Also