gene_sets

This is data to be included in package

datasets

A method that inherits the standard gene set variation analysis (GSVA) method and also provides the option to use summary statistics from any analysis (disease vs healthy, lesional side vs nonlesional side, etc..) input to define the direction of gene sets used for directional gene set score calculation for a given disease. Note to use this package, GSVA(>= 1.52.1) is needed to pre-installed.
Hanzelmann, S., Castelo, R., and Guinney, J. (2013) <doi:10.1186/1471-2105-14-7>.

Xingpeng Li

ssdGSA

Single Sample Directional Gene Set Analysis

Qi Qian

gene_sets function

An example disease gene sets in the form of a list, with gene set names as list component names,
and each component is a vector of gene entrez ID. In this sample gene sets list, there are 10 gene sets in total.<dl>
<dt>TCELL.KEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY</dt>
<dd>gene entrez ID related to this pathway</dd><dt>TLR.KEGG_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY</dt>
<dd>gene entrez ID related to this pathway</dd><dt>BCELL.KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY</dt>
<dd>gene entrez ID related to this pathway</dd><dt>NEUROTROPHIN.KEGG_NEUROTROPHIN_SIGNALING_PATHWAY</dt>
<dd>gene entrez ID related to this pathway</dd><dt>ERBB.KEGG_ERBB_SIGNALING_PATHWAY</dt>
<dd>gene entrez ID related to this pathway</dd><dt>CALCIUM.KEGG_CALCIUM_SIGNALING_PATHWAY</dt>
<dd>gene entrez ID related to this pathway</dd><dt>CHEMOKINE.KEGG_CHEMOKINE_SIGNALING_PATHWAY</dt>
<dd>gene entrez ID related to this pathway</dd><dt>GNRH.KEGG_GNRH_SIGNALING_PATHWAY</dt>
<dd>gene entrez ID related to this pathway</dd><dt>VEGF.KEGG_VEGF_SIGNALING_PATHWAY</dt>
<dd>gene entrez ID related to this pathway</dd>
</dl>

Format

This is data to be included in package — gene_sets

An example disease gene sets in the form of a list, with gene set names as list component names,
and each component is a vector of gene entrez ID. In this sample gene sets list, there are 10 gene sets in total.<dl>
<dt>TCELL.KEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY</dt>
<dd>gene entrez ID related to this pathway</dd>

<dt>TLR.KEGG_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY</dt>
<dd>gene entrez ID related to this pathway</dd>

<dt>BCELL.KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY</dt>
<dd>gene entrez ID related to this pathway</dd>

<dt>NEUROTROPHIN.KEGG_NEUROTROPHIN_SIGNALING_PATHWAY</dt>
<dd>gene entrez ID related to this pathway</dd>

<dt>ERBB.KEGG_ERBB_SIGNALING_PATHWAY</dt>
<dd>gene entrez ID related to this pathway</dd>

<dt>CALCIUM.KEGG_CALCIUM_SIGNALING_PATHWAY</dt>
<dd>gene entrez ID related to this pathway</dd>

<dt>CHEMOKINE.KEGG_CHEMOKINE_SIGNALING_PATHWAY</dt>
<dd>gene entrez ID related to this pathway</dd>

<dt>GNRH.KEGG_GNRH_SIGNALING_PATHWAY</dt>
<dd>gene entrez ID related to this pathway</dd>

<dt>VEGF.KEGG_VEGF_SIGNALING_PATHWAY</dt>
<dd>gene entrez ID related to this pathway</dd>


</dl>

gene_sets: This is data to be included in package

Description

Usage

Arguments

Format