getPval-methods: Extract tissue/geneset enrichment p-value distribution from...

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

Description

This function extracts the enrichment p-value distribution from eQTL list query result. P-values from different tissues/cell types are organized, and QQ-plot is generated against uniform distribution

Usage

getPval(res, ...)

## S4 method for signature 'loci2pathResult'
getPval(res, test.method = c("gene", "eqtl",
  "glm"))

Arguments

res	query result from function query.egset.list()
...	additional params
test.method	Choose which enrichment test should be used to retrive p-values from. Options include:"gene"(default, gene-based fisher's exact test),"eqtl" (eqtl based fisher's exact test), "glm" (ordered query)

Value

generate pval distribution plot

Examples

result <- query(query.gr=query.gr, 
  loci=eset.list, path=biocarta)
getPval(result, test.method="gene")

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