miRNApath: miRNApath: Pathway Enrichment for miRNA Expression Data
Version 1.36.0

This package provides pathway enrichment techniques for miRNA expression data. Specifically, the set of methods handles the many-to-many relationship between miRNAs and the multiple genes they are predicted to target (and thus affect.) It also handles the gene-to-pathway relationships separately. Both steps are designed to preserve the additive effects of miRNAs on genes, many miRNAs affecting one gene, one miRNA affecting multiple genes, or many miRNAs affecting many genes.

Browse man pages Browse package API and functions Browse package files

AuthorJames M. Ward <jmw86069@gmail.com> with contributions from Yunling Shi, Cindy Richards, John P. Cogswell
Bioconductor views Annotation DifferentialExpression NetworkEnrichment Pathways miRNA
Date of publicationNone
MaintainerJames M. Ward <jmw86069@gmail.com>
LicenseLGPL-2.1
Version1.36.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("miRNApath")

Man pages

checkColumns: Check data.frame for Required Columns
convertFoldChange: Converts Fold Change to Consistent Format
filtermirnapath: Filter miRNApath data
loadmirnapath: Load miRNApath Data
loadmirnapathways: Load gene to pathway associations for miRNApath
loadmirnatogene: Load miRNA to gene associations for miRNApath
mirnaobj: mirnaobj, an S4 object of class "mirnapath"
mirnapath-class: S4 class mirnapath and its "show" method
miRNApath-package: miRNApath: Pathway Enrichment for miRNA Expression Data
mirnaTable: Create miRNA Enrichment Summary Table as data.frame
runEnrichment: Perform gene set enrichment analysis on a miRNApath object

Functions

checkColumns Man page
convertFoldChange Man page
filtermirnapath Man page
loadmirnapath Man page
loadmirnapathways Man page
loadmirnatogene Man page
miRNApath-package Man page
mirnaTable Man page
mirnaobj Man page
mirnapath-class Man page
runEnrichment Man page
show,mirnapath-method Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/checkColumns.R
R/convertFoldChange.R
R/filtermirnapath.R
R/loadmirnapath.R
R/loadmirnapathways.R
R/loadmirnatogene.R
R/mirnaTable.R
R/runEnrichment.R
R/show.mirnapath.R
build
build/vignette.rds
data
data/mirnaobj.rda
inst
inst/CITATION
inst/doc
inst/doc/miRNApath.R
inst/doc/miRNApath.Rnw
inst/doc/miRNApath.pdf
inst/samples
inst/samples/ADmiRNA.pdf
man
man/checkColumns.Rd
man/convertFoldChange.Rd
man/filtermirnapath.Rd
man/loadmirnapath.Rd
man/loadmirnapathways.Rd
man/loadmirnatogene.Rd
man/miRNApath-package.Rd
man/mirnaTable.Rd
man/mirnaobj.Rd
man/mirnapath-class.Rd
man/runEnrichment.Rd
vignettes
vignettes/miRNApath.Rnw
miRNApath documentation built on May 20, 2017, 11:02 p.m.