Function reference • linkage

All functions

AnnoUpsetPlot(): AnnoUpsetPlot

BuildNetwork(): BuildNetwork.

CombinePlots(): Combine ggplot2-based plots into a single plot

CorrPlot(): Correlation scatter plot.

CreateLinkageObject(): Create a Linkage Object

CreateNetworkObject(): Create Network Object.

EnrichBarPlot(): Enrichment analysis Barplot

EnrichCnetPlot(): Enrichment analysis Cnetplot

EnrichDotPlot(): Enrichment analysis Dotplot

EnrichUpsetPlot(): Enrichment analysis Upsetplot

EnrichWordCloud(): Enrichment analysis Wordcloud

GOEnrichment(): GO enrichment analysis

Homo.position Homo.position: Homo sapiens genetic coordinates

Install.biocViews(): Used when the linkage is installed for the first time and is used to install dependencies

KEGGEnrichment(): KEGG enrichment analysis

Linkage.UIO(): Launch Linkage Shiny App

LinkageObject-class: Linkage Class

MultipleMotifAnalysis(): MotifAnalysis.

Mus.PFMatrixList: Mus musculus sapiens PWM matrix list of motif

Mus.position: Mus musculus sapiens genetic coordinates

Mus.pwm_library_dt: Mus musculus sapiens motif id and name

PeakAnnottation(): Annotation regulatory peak

PFMatrixList: Homo sapiens PWM matrix list of motif

pwm_library_dt: Homo sapiens motif id and name

RegulatoryPeak(): Finding the regulatory peak of genes.

SeqLogoPlot(): Transcription factor Seqlogo plot.

SingleMotifAnalysis(): Regulatory peak motif enrichment analysis

SmallLinkageObject: An small LinkageObject with 5 genes and 3982 peaks

TrackPlot(): TrackPlot