Function reference • Linkage

All functions

AnnoUpsetPlot(): AnnoUpsetPlot

BuildGRNs(): MotifAnalysis.

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

CorrPlot(): Correlation scatter plot.

CreateLinkageObject(): Create a Linkage Object

EnrichBarPlot(): Enrichment analysis Barplot

EnrichCnetPlot(): Enrichment analysis Cnetplot

EnrichDotPlot(): Enrichment analysis Dotplot

EnrichUpsetPlot(): Enrichment analysis Upsetplot

EnrichWordCloud(): Enrichment analysis Wordcloud

FilterGRNs(): Create Network Object.

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

MotifEnrichment(): Regulatory peak motif enrichment analysis

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

PeakAnnotation(): 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.

SASPGeneSet: Senescence-associated secretory phenotype Gene Set

SeqLogoPlot(): Transcription factor Seqlogo plot.

SmallLinkageObject: An small LinkageObject with 5 genes and 3982 peaks

Small_ATAC: Small ATAC-seq count

Small_RNA: Small RNA-seq count

TrackPlot(): TrackPlot

VisualGRNs(): VisualGRNs.