| Title: | 'Grouphmap' is an Automated One-Step Common Analysis of Batch Expression Profile |
|---|---|
| Description: | 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. |
| Authors: | Yuchen Sun [aut, cre] |
| Maintainer: | Yuchen Sun <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 1.0.0 |
| Built: | 2025-02-22 04:41:58 UTC |
| Source: | https://github.com/cran/Grouphmap |
Grouphmap: Automated one-step common analysis of Batch expression profile
ghmap(Path, conRep, treRep, OrgDb, TYPE, UP = TRUE, cutree, TOP)ghmap(Path, conRep, treRep, OrgDb, TYPE, UP = TRUE, cutree, TOP)
Path |
"File storage path." Two groups are one file, and the control group should before the treatment group. |
conRep |
Number of repetitions in control group. |
treRep |
Number of repetitions in treatment group. |
OrgDb |
org.Mm.eg.db, org.Hs.eg.db, and org.Sc.sgd.db. Please library(). |
TYPE |
"SYMBOL","ENSEMBOL"... |
UP |
up is TRUE and down is FALSE |
cutree |
heatmap can be devided multiple modules that make the functional difference and similarity of those group to be obvious |
TOP |
the numeric.Such as 10 is the top 10 of GO analysis in each file. |
p1
library(org.Mm.eg.db) Path<-system.file("extdata", package = "Grouphmap") ghmap(Path,2,2,org.Mm.eg.db,"ENSEMBL",FALSE,2,10)library(org.Mm.eg.db) Path<-system.file("extdata", package = "Grouphmap") ghmap(Path,2,2,org.Mm.eg.db,"ENSEMBL",FALSE,2,10)