MiRSEA: 'MicroRNA' Set Enrichment Analysis

The tools for 'MicroRNA Set Enrichment Analysis' can identify risk pathways(or prior gene sets) regulated by microRNA set in the context of microRNA expression data. (1) This package constructs a correlation profile of microRNA and pathways by the hypergeometric statistic test. The gene sets of pathways derived from the three public databases (Kyoto Encyclopedia of Genes and Genomes ('KEGG'); 'Reactome'; 'Biocarta') and the target gene sets of microRNA are provided by four databases('TarBaseV6.0'; 'mir2Disease'; 'miRecords'; 'miRTarBase';). (2) This package can quantify the change of correlation between microRNA for each pathway(or prior gene set) based on a microRNA expression data with cases and controls. (3) This package uses the weighted Kolmogorov-Smirnov statistic to calculate an enrichment score (ES) of a microRNA set that co-regulate to a pathway , which reflects the degree to which a given pathway is associated with the specific phenotype. (4) This package can provide the visualization of the results.

Author
Junwei Han, Siyao Liu
Date of publication
2015-07-01 11:30:03
Maintainer
Junwei Han <hanjunwei1981@163.com>
License
GPL (>= 2)
Version
1.1

View on CRAN

Man pages

Corrp2miRfile
create a pathway-microRNA(miRNA) profile and a p value matrix
EnrichmentScore
Computes the enrichment score
EnrichmentScore2
Computes the enrichment score faster
envData
The variables in the environment include predefine pathway,...
GetExampleData
Get the example data
GetMiRTargetData
Get the data of microRNA(miRNA) and target genes
GetPathwayData
Get the gene sets of pathways
HeatMapPlot
Plot a heatmap
MirSEA
Identify dysregulated pathways based on microRNA (miRNA) set...
MiRSEA-internal
MiRSEA internal functions
MiRSEA-package
MicroRNA Set Enrichment Analysis
MsReport
Produce report for a microRNA (abbreviated miRNA) set
PlotCorrelation
Plot global microRNA(miRNA) correlation profile
PlotHeatMap
Plot a heat map
PlotRunEnrichment
Plot running microRNAs(miRNAs) enrichment score
S2N
calculate signal to noise ratio for microRNAs(miRNAs)

Files in this package

MiRSEA
MiRSEA/inst
MiRSEA/inst/localdata
MiRSEA/inst/localdata/example.gct
MiRSEA/inst/localdata/example.cls.cls
MiRSEA/inst/doc
MiRSEA/inst/doc/MiRSEA.Rnw
MiRSEA/inst/doc/MiRSEA.pdf
MiRSEA/NAMESPACE
MiRSEA/data
MiRSEA/data/envData.rda
MiRSEA/R
MiRSEA/R/PlotHeatMap.R
MiRSEA/R/MsReport.R
MiRSEA/R/Corrp2miRfile.R
MiRSEA/R/GetMiRTargetData.R
MiRSEA/R/GetExampleData.R
MiRSEA/R/S2N.R
MiRSEA/R/EnrichmentScore.R
MiRSEA/R/PlotRunEnrichment.R
MiRSEA/R/GetPathwayData.R
MiRSEA/R/MirSEA.R
MiRSEA/R/getEnvironmentData.R
MiRSEA/R/PlotCorrelation.R
MiRSEA/vignettes
MiRSEA/vignettes/MiRSEA.Rnw
MiRSEA/MD5
MiRSEA/DESCRIPTION
MiRSEA/man
MiRSEA/man/PlotCorrelation.Rd
MiRSEA/man/S2N.Rd
MiRSEA/man/PlotHeatMap.Rd
MiRSEA/man/MiRSEA-package.Rd
MiRSEA/man/EnrichmentScore.Rd
MiRSEA/man/EnrichmentScore2.Rd
MiRSEA/man/MirSEA.Rd
MiRSEA/man/HeatMapPlot.Rd
MiRSEA/man/MiRSEA-internal.Rd
MiRSEA/man/envData.Rd
MiRSEA/man/Corrp2miRfile.Rd
MiRSEA/man/MsReport.Rd
MiRSEA/man/GetMiRTargetData.Rd
MiRSEA/man/PlotRunEnrichment.Rd
MiRSEA/man/GetExampleData.Rd
MiRSEA/man/GetPathwayData.Rd