pathwayanalysis: Run Overrepresentation Analysis via the ClusterProfiler...
In FerrenaAlexander/FerrenaBulkRNAseq: Pipeline for analysis of bulkRNAseq data
View source: R/pathwayanalysis.R
pathwayanalysis R Documentation
Run Overrepresentation Analysis via the ClusterProfiler workflow
Description
Run Overrepresentation Analysis via the ClusterProfiler workflow
Usage
pathwayanalysis(sigres, term2gene)
Arguments
sigres
data.frame of significant genes. first column is gene names; second column is logfoldchange or other effect size.
term2gene
data.frame of pathways to check. first column is pathways, second column is genes.
Value
a list object: first element is a ClusterProfiler object; second element is an "emap plot", a graph of pathways connected by jaccard similarity; third element is a data.frame with the connected nodes from the emap plot; 4th element is a list of pathways in each connected cluster; 5th element is genes from the pathways in each cluster
FerrenaAlexander/FerrenaBulkRNAseq documentation built on Oct. 16, 2022, 8:18 a.m.
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View source: R/pathwayanalysis.R
| pathwayanalysis | R Documentation |
Run Overrepresentation Analysis via the ClusterProfiler workflow
Description
Run Overrepresentation Analysis via the ClusterProfiler workflow
Usage
pathwayanalysis(sigres, term2gene)
Arguments
sigres |
data.frame of significant genes. first column is gene names; second column is logfoldchange or other effect size. |
term2gene |
data.frame of pathways to check. first column is pathways, second column is genes. |
Value
a list object: first element is a ClusterProfiler object; second element is an "emap plot", a graph of pathways connected by jaccard similarity; third element is a data.frame with the connected nodes from the emap plot; 4th element is a list of pathways in each connected cluster; 5th element is genes from the pathways in each cluster
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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