| Type: | Package |
| Title: | 'Grouphmap' is an Automated One-Step Common Analysis of Batch Expression Profile |
| Version: | 1.0.0 |
| Author: | Yuchen Sun [aut, cre] |
| Maintainer: | Yuchen Sun <yuchensun2436@163.com> |
| Depends: | R (≥ 4.2.0) |
| 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. |
| License: | Artistic-2.0 |
| Encoding: | UTF-8 |
| Imports: | limma, clusterProfiler, dplyr, org.Mm.eg.db, pheatmap, stringr, stats, utils, grDevices |
| RoxygenNote: | 7.2.3 |
| References: | Matthew E Ritchie , Belinda Phipson , Di Wu , Yifang Hu , Charity W Law , Wei Shi , Gordon K Smyth (2015) <doi:10.1093/nar/gkv007>; Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He (2012) <doi:10.1089/omi.2011.0118> |
| NeedsCompilation: | no |
| Packaged: | 2023-09-04 02:24:10 UTC; yuchensun |
| Repository: | CRAN |
| Date/Publication: | 2023-09-04 09:50:02 UTC |
Grouphmap: Automated one-step common analysis of Batch expression profile
Description
Grouphmap: Automated one-step common analysis of Batch expression profile
Usage
ghmap(Path, conRep, treRep, OrgDb, TYPE, UP = TRUE, cutree, TOP)
Arguments
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. |
Value
p1
Examples
library(org.Mm.eg.db)
Path<-system.file("extdata", package = "Grouphmap")
ghmap(Path,2,2,org.Mm.eg.db,"ENSEMBL",FALSE,2,10)