ghmap

Grouphmap: Automated one-step common analysis of Batch expression profile

The 'Grouphmap' was implemented in R, an open-source programming environment, and was released under the provided website. The difference analysis is based on the 'limma' package, which can cover gene and protein expression profiles (Reference: Matthew E Ritchie , Belinda Phipson , Di Wu , Yifang Hu , Charity W Law , Wei Shi , Gordon K Smyth (2015) <doi:10.1093/nar/gkv007>). The GO enrichment analysis is based on the 'clusterProfiler' package and supports three common species: human, mouse, and yeast (Reference: Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He (2012) <doi:10.1089/omi.2011.0118>). The results of batch difference analysis and enrichment analysis are output in separate folders for easy viewing and further visualization of the results during the process. The results returned a heatmap in R and exported to 3 folders named DEG, go, and merge.

Yuchen Sun

Grouphmap

'Grouphmap' is an Automated One-Step Common Analysis of Batch
Expression Profile

ghmap function

<dl><dt>Path</dt>
<dd>"File storage path." Two groups are one file, and the control group should before the treatment group.</dd>
<dt>conRep</dt>
<dd>Number of repetitions in control group.</dd>
<dt>treRep</dt>
<dd>Number of repetitions in treatment group.</dd>
<dt>OrgDb</dt>
<dd>org.Mm.eg.db, org.Hs.eg.db, and org.Sc.sgd.db. Please library().</dd>
<dt>TYPE</dt>
<dd>"SYMBOL","ENSEMBOL"...</dd>
<dt>UP</dt>
<dd>up is TRUE and down is FALSE</dd>
<dt>cutree</dt>
<dd>heatmap can be devided multiple modules that make the functional difference and similarity of those group to be obvious</dd>
<dt>TOP</dt>
<dd>the numeric.Such as 10 is the top 10 of GO analysis in each file.</dd></dl>

Arguments

Grouphmap: Automated one-step common analysis of Batch expression profile — ghmap

<dl>

<dt>Path</dt>
<dd>"File storage path." Two groups are one file, and the control group should before the treatment group.</dd>


<dt>conRep</dt>
<dd>Number of repetitions in control group.</dd>


<dt>treRep</dt>
<dd>Number of repetitions in treatment group.</dd>


<dt>OrgDb</dt>
<dd>org.Mm.eg.db, org.Hs.eg.db, and org.Sc.sgd.db. Please library().</dd>


<dt>TYPE</dt>
<dd>"SYMBOL","ENSEMBOL"...</dd>


<dt>UP</dt>
<dd>up is TRUE and down is FALSE</dd>


<dt>cutree</dt>
<dd>heatmap can be devided multiple modules that make the functional difference and similarity of those group to be obvious</dd>


<dt>TOP</dt>
<dd>the numeric.Such as 10 is the top 10 of GO analysis in each file.</dd>

</dl>

ghmap: Grouphmap: Automated one-step common analysis of Batch expression profile

Description

Usage

Value

Arguments

Examples