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

Description Usage Arguments Value Examples

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

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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

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

StanleyXu/egquery documentation built on Sept. 12, 2019, 9:35 a.m.