Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs

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Documentation for package ‘loci2path’ version 1.22.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

biocarta	eQTL geneset enrichment query demo data
check.geneid	check compatibility of gene identifiers between eQTL set and gene set
coveredGene	loci2pathResult Class
coveredGene-method	loci2pathResult Class
description	geneSet Class
description-method	geneSet Class
eqtlGene	eqtlSet Class
eqtlGene-method	eqtlSet Class
eqtlId	eqtlSet Class
eqtlId-method	eqtlSet Class
eqtlRange	eqtlSet Class
eqtlRange-method	eqtlSet Class
eqtlSet	eqtlSet Class
eqtlSet-class	eqtlSet Class
eset.list	eQTL geneset enrichment query demo data
geneSet	geneSet Class
geneSet-class	geneSet Class
geneSetList	geneSet Class
geneSetList-method	geneSet Class
getHeatmap	Generate heatmap of enrichment matrix from query result
getHeatmap-method	Generate heatmap of enrichment matrix from query result
getMat	Extract tissue/geneset enrichment matrix from query result
getMat-method	Extract tissue/geneset enrichment matrix from query result
getPathDescription	Extract description for enriched pathways from query result and geneSet object
getPathDescription-method	Extract description for enriched pathways from query result and geneSet object
getPval	Extract tissue/geneset enrichment p-value distribution from query result
getPval-method	Extract tissue/geneset enrichment p-value distribution from query result
getTissueDegree	Extract tissue degree from query result
getTissueDegree-method	Extract tissue degree from query result
getWordcloud	Plot word cloud using frequent terms of pathways and genes
getWordcloud-method	Plot word cloud using frequent terms of pathways and genes
loci2pathResult	loci2pathResult Class
loci2pathResult-class	loci2pathResult Class
numGene	geneSet Class
numGene-method	geneSet Class
query	Query enrichment in geneset through multiple eQTL sets.
query-method	Query enrichment in geneset through multiple eQTL sets.
query.gr	eQTL geneset enrichment query demo data
resultTable	loci2pathResult Class
resultTable-method	loci2pathResult Class
tissue	eqtlSet Class
tissue-method	eqtlSet Class