get_biomart_mapping

Internal function for obtaining biomaRt mapping

internal

Integrates pathway information into the differential network analysis of two gene expression datasets as described in Grimes, Potter, and Datta (2019) <doi:10.1038/s41598-019-41918-3>. Provides summary functions to break down the results at the pathway, gene, or individual connection level. The differential networks for each pathway of interest can be plotted, and the visualization will highlight any differentially expressed genes and all of the gene-gene associations that are significantly differentially connected.

Tyler Grimes

dnapath

Differential Network Analysis using Gene Pathways

Somnath Datta

get_biomart_mapping function

<dl><dt>species</dt>
<dd>The species to obtain a biomart dataset for. This should be
an output from <code>format_species_name</code>.</dd>
<dt>symbol_name</dt>
<dd>The type of gene symbol to use. HGNC symbols are used by
default (hgnc_symbol), unless <code>species</code> is "mmusculus", in which case MGI
symbols are used (mgi_symbol).</dd>
<dt>dir_save</dt>
<dd>The directory to store annotation reference. Future
calls to this function will use the stored annotations. This speeds up the
operation and allows for reproducibility in the event that the <code>biomaRt</code>
database is updated. Set to NULL to disable. By default, it uses a
temporary directory to store files during the R session.</dd>
<dt>verbose</dt>
<dd>Set to FALSE to avoid messages.</dd></dl>

Arguments

Internal function for obtaining biomaRt mapping — get_biomart_mapping

<dl>

<dt>species</dt>
<dd>The species to obtain a biomart dataset for. This should be
an output from <code>format_species_name</code>.</dd>


<dt>symbol_name</dt>
<dd>The type of gene symbol to use. HGNC symbols are used by
default (hgnc_symbol), unless <code>species</code> is "mmusculus", in which case MGI
symbols are used (mgi_symbol).</dd>


<dt>dir_save</dt>
<dd>The directory to store annotation reference. Future
calls to this function will use the stored annotations. This speeds up the
operation and allows for reproducibility in the event that the <code>biomaRt</code>
database is updated. Set to NULL to disable. By default, it uses a
temporary directory to store files during the R session.</dd>


<dt>verbose</dt>
<dd>Set to FALSE to avoid messages.</dd>

</dl>

get_biomart_mapping: Internal function for obtaining biomaRt mapping

Description

Usage

Value

Arguments