getReactome

Get Reactome geneset and geneset_name
Geneset is a data.frame of 2 columns with term id and gene id;
Geneset_name is a data.frame of 2 columns with term id and term description

Gene sets are fundamental for gene enrichment analysis. The package 'geneset' enables querying
gene sets from public databases including 'GO' (Gene Ontology Consortium. (2004) <doi:10.1093/nar/gkh036>),
'KEGG' (Minoru et al. (2000) <doi:10.1093/nar/28.1.27>),
'WikiPathway' (Marvin et al. (2020) <doi:10.1093/nar/gkaa1024>),
'MsigDb' (Arthur et al. (2015) <doi:10.1016/j.cels.2015.12.004>),
'Reactome' (David et al. (2011) <doi:10.1093/nar/gkq1018>),
'MeSH' (Ish et al. (2014) <doi:10.4103/0019-5413.139827>),
'DisGeNET' (Janet et al. (2017) <doi:10.1093/nar/gkw943>),
'Disease Ontology' (Lynn et al. (2011) <doi:10.1093/nar/gkr972>),
'Network of Cancer Genes' (Dimitra et al. (2019) <doi:10.1186/s13059-018-1612-0>) and
'COVID-19' (Maxim et al. (2020) <doi:10.21203/rs.3.rs-28582/v1>).
Gene sets are stored in the list object which provides data frame of 'geneset' and 'geneset_name'.
The 'geneset' has two columns of term ID and gene ID. The 'geneset_name' has two columns of
terms ID and term description.

Yunze Liu

geneset

Get Gene Sets for Gene Enrichment Analysis

getReactome function

<dl><dt>org</dt>
<dd>Organism name from `reactome_org`.</dd>
<dt>download.method</dt>
<dd>"auto" (as default if NULL), "wininet" (for windows)</dd>
<dt>data_dir</dt>
<dd>data saving location, default is the package data directory</dd></dl>

Arguments

Get Reactome geneset and geneset_name
Geneset is a data.frame of 2 columns with term id and gene id;
Geneset_name is a data.frame of 2 columns with term id and term description — getReactome

<dl>

<dt>org</dt>
<dd>Organism name from `reactome_org`.</dd>


<dt>download.method</dt>
<dd>"auto" (as default if NULL), "wininet" (for windows)</dd>


<dt>data_dir</dt>
<dd>data saving location, default is the package data directory</dd>

</dl>

Get Reactome geneset and geneset_name
Geneset is a data.frame of 2 columns with term id and gene id;
Geneset_name is a data.frame of 2 columns with term id and term description

getReactome: Get Reactome geneset and geneset_name Geneset is a data.frame of 2 columns with term id and gene id; Geneset_name is a data.frame of 2 columns with term id and term description

Description

Usage

Value

Arguments

Examples