comGeneSet: Performing Geneset-based pathway ranking (ORA & GSEA) with...
In Mathlida/comPath: Integrating proteomic and phosphoproteomic data for pathway analysis
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
Description
A function performs Geneset-based pathway ranking (ORA & GSEA) with integrated data
Usage
1
GeneSetcom(DEexpression)
Arguments
DEexpression
Six variables including all expressed proteins and phosphoproteins, their differential expression and the fold change of the differential expression.
Details
Intersection of the differentially expressed proteins and phosphoproteins, the sum of the fold change absolute value of protein and phosphoptrotein are set as the input for Geneset-based pathway analysis. Permutations for deriving p-values in Geneset-based pathway analysis is 2000. The p value adjust method is "Benjamini & Hochberg" (p < 0.05). The protein/phosphoprotein ID is Entrez gene ID.
Value
The rankings and the significance of pathways with ORA and GSEA methods.
Author(s)
Jie Ren, Jing Li
See Also
help(HTSanalyzeR)
Examples
1
2
3
Gsetresults <- GeneSetcom(DEexpression)
ORAresult <- Gsetresults@result$HyperGeo.results$PW_KEGG
GSEAresult <- Gsetresults@result$GSEA.results$PW_KEGG
Mathlida/comPath documentation built on May 23, 2019, 5:03 p.m.
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Description Usage Arguments Details Value Author(s) See Also Examples
Description
A function performs Geneset-based pathway ranking (ORA & GSEA) with integrated data
Usage
1 | GeneSetcom(DEexpression)
|
Arguments
DEexpression |
Six variables including all expressed proteins and phosphoproteins, their differential expression and the fold change of the differential expression. |
Details
Intersection of the differentially expressed proteins and phosphoproteins, the sum of the fold change absolute value of protein and phosphoptrotein are set as the input for Geneset-based pathway analysis. Permutations for deriving p-values in Geneset-based pathway analysis is 2000. The p value adjust method is "Benjamini & Hochberg" (p < 0.05). The protein/phosphoprotein ID is Entrez gene ID.
Value
The rankings and the significance of pathways with ORA and GSEA methods.
Author(s)
Jie Ren, Jing Li
See Also
help(HTSanalyzeR)
Examples
1 2 3 | Gsetresults <- GeneSetcom(DEexpression)
ORAresult <- Gsetresults@result$HyperGeo.results$PW_KEGG
GSEAresult <- Gsetresults@result$GSEA.results$PW_KEGG
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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