loci2pathResult-class: loci2pathResult Class

In StanleyXu/loci2path: Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs

Description

loci2pathResult Class contains information for the query result from query function query. Result object contains a ranked pathway table, and a vector of gene names that are associated with loci covered by query regions

Usage

resultTable(x)

coveredGene(x)

## S4 method for signature 'loci2pathResult'
resultTable(x)

## S4 method for signature 'loci2pathResult'
coveredGene(x)

Arguments

x	An geneSet object

Value

Object of CLass loci2pathResult

Slots

resultTable

data.frame; contains enrichment statistics, summary of eQTL and gene numbers, pathway names and gene names, etc.

coveredGene

list; each member is a vector of genes associated with one tissue, whose associating loci are covered by query regions

Examples

result <- query(query.gr=query.gr, 
  loci=eset.list, path=biocarta)
result
resultTable(result) # a data.frame for enriched pathways
coveredGene(result)  

StanleyXu/loci2path documentation built on Sept. 11, 2019, 8:21 a.m.