GSEA: GSEA
In cinaR: A Computational Pipeline for Bulk 'ATAC-Seq' Profiles
View source: R/enrichment_functions.R
GSEA R Documentation
GSEA
Description
Gene set enrichment analyses, runs 'fgsea' package implementation with preset values.
Usage
GSEA(genes, geneset)
Arguments
genes
DA gene names to be checked if they are over-represented or not.
geneset
Pathways to be used in enrichment analyses. If not set vp2008 (Chaussabel, 2008)
immune modules will be used. This can be set to any geneset using 'read.gmt' function from 'qusage'
package. Different modules are available: https://www.gsea-msigdb.org/gsea/downloads.jsp.
Value
data.frame, list of pathways and their enrichment (adjusted) p-values.
References
G. Korotkevich, V. Sukhov, A. Sergushichev. Fast gene set enrichment analysis. bioRxiv (2019),
doi:10.1101/060012
Examples
library(cinaR)
library(fgsea)
data(examplePathways)
data(exampleRanks)
GSEA(exampleRanks, examplePathways)
cinaR documentation built on May 18, 2022, 5:12 p.m.
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View source: R/enrichment_functions.R
| GSEA | R Documentation |
GSEA
Description
Gene set enrichment analyses, runs 'fgsea' package implementation with preset values.
Usage
GSEA(genes, geneset)
Arguments
genes |
DA gene names to be checked if they are over-represented or not. |
geneset |
Pathways to be used in enrichment analyses. If not set vp2008 (Chaussabel, 2008) immune modules will be used. This can be set to any geneset using 'read.gmt' function from 'qusage' package. Different modules are available: https://www.gsea-msigdb.org/gsea/downloads.jsp. |
Value
data.frame, list of pathways and their enrichment (adjusted) p-values.
References
G. Korotkevich, V. Sukhov, A. Sergushichev. Fast gene set enrichment analysis. bioRxiv (2019), doi:10.1101/060012
Examples
library(cinaR) library(fgsea) data(examplePathways) data(exampleRanks) GSEA(exampleRanks, examplePathways)
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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