getSPIAKEGGNetwork

Get KEGG pathway network for SPIA method

Provides a set of functions to perform pathway analysis and meta-analysis from multiple gene expression datasets, as well as visualization of the results. This package wraps functionality from the following packages: Ritchie et al. (2015) <doi:10.1093/nar/gkv007>, Love et al. (2014) <doi:10.1186/s13059-014-0550-8>, Robinson et al. (2010) <doi:10.1093/bioinformatics/btp616>, Korotkevich et al. (2016) <arxiv:10.1101/060012>, Efron et al. (2015) <https://CRAN.R-project.org/package=GSA>, and Gu et al. (2012) <https://CRAN.R-project.org/package=CePa>.

Ha Nguyen

RCPA

Consensus Pathway Analysis

Phi Bya

Zeynab Maghsoudi

Tin Nguyen

getSPIAKEGGNetwork function

<dl><dt>org</dt>
<dd>The organism abbreviation. E.g, hsa, mmu, dme, etc.
To see the full list of supported organisms, visit https://www.genome.jp/kegg/catalog/org_list.html.</dd>
<dt>updateCache</dt>
<dd>A parameter to disable/enable cache update.</dd></dl>

Arguments

Get KEGG pathway network for SPIA method — getSPIAKEGGNetwork

<dl>

<dt>org</dt>
<dd>The organism abbreviation. E.g, hsa, mmu, dme, etc.
To see the full list of supported organisms, visit https://www.genome.jp/kegg/catalog/org_list.html.</dd>


<dt>updateCache</dt>
<dd>A parameter to disable/enable cache update.</dd>

</dl>

getSPIAKEGGNetwork: Get KEGG pathway network for SPIA method

Description

Usage

Value

Arguments

Examples