comPath: Integrating proteomic and phosphoproteomic data for pathway...

In Mathlida/comPath: Integrating proteomic and phosphoproteomic data for pathway analysis

Description

A package Integrates proteomic and phosphoproteomic data for pathway analysis, evaluates and visualizes the different imapcts between proteome and phosphoproteome on a disturbed pathway.

Details

Package:	SeqMADE
Type:	Package
Version:	1.0
Date:	2018-08-14
LazyLoad:	yes

The main functions in this package are: Dexpress is a function of identifying the differentially expressed proteins and phosphoproteins and their fold change. GeneSetcom is a function of performing Geneset-based pathway ranking (ORA & GSEA) with integrated data. SPIAcom is a function of performing topology-based pathway ranking (SPIA) with integrated data. impact is a function of evaluating and visualizing the different impacts between proteins and phosphoproteins on a disturbed pathway.

Author(s)

Jie Ren, Jing Li. Maintainer: JieRen<[e-mail]>

References

Ren, J., Wang, B. and Li, J.Integrating proteomic and phosphoproteomic data for pathway analysis in breast cancer. BMC Systems Biology2018,12 (Suppl 8):130

See Also

help(SPIA), help(HTSanalyzeR)

Examples

data(exprs)
data(phosexprs)
case=c("A1","A2","A3","A4","A5","A6","A7","A8","A9","A10")
ctrl=c("B1","B2","B3")
DEexpression=Dexpress(exprs,phosexprs,case,ctrl)
summary(DEexpression)
Gsetresults <- GeneSetcom(DEexpression)
ORAresult <- Gsetresults@result$HyperGeo.results$PW_KEGG
GSEAresult <- Gsetresults@result$GSEA.results$PW_KEGG
SPIAresults <- SPIAcom(DEexpression)

Mathlida/comPath documentation built on May 23, 2019, 5:03 p.m.