getMat-methods: Extract tissue/geneset enrichment matrix from query result

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

Description

This function extracts the enrichment matrix from eQTL list query result. The rows of the matrixs are pathways; and the columns of the matrixs are tissues/cell lines of the eQTL sets. P-Values from enrichment tests are summarized in this matrix

Usage

getMat(res, ...)

## S4 method for signature 'loci2pathResult'
getMat(res, test.method = c("gene", "eqtl",
  "glm"), filter.quantile = 0.5, max.ptw.gene = 5000)

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)
filter.quantile	Filter option; choose the max quantile of all p-values being kept in the matrix; default is 0.5, which means p-values larger than median p-values are discarded
max.ptw.gene	Filter option; minimum number of genes in a pathway; default is 5000 (pathway with >5000 genes are not included in the matrix)

Value

p-value matrix collected from enrichment result table

Examples

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

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