getTissueDegree-methods: Extract tissue degree from query result

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

Description

This function extracts the tissue degree from eQTL list query result for each pathway.

Usage

getTissueDegree(res, ...)

## S4 method for signature 'loci2pathResult'
getTissueDegree(res, loci)

Arguments

res	query result from function query.egset.list()
...	additional params
loci	a list of eqtlSet; each member should be an eqtlSet object

Value

gene.tissue.map	shows mapping:gene<->tissue
gene.tissue.degree	shows tissue degree for each gene
mean.tissue.degree	shows the average tissue digree for each pathway in the result table

Examples

result <- query(query.gr=query.gr, 
  loci=eset.list, path=biocarta)
tissue.degree=getTissueDegree(result, eset.list)
head(tissue.degree$gene.tissue.map)
head(tissue.degree$gene.tissue.degree)
head(tissue.degree$mean.tissue.degree)

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