getHeatmap-methods: Generate heatmap of enrichment matrix from query result

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

Description

This function generate the enrichment heatmap using pheatmap package.

Usage

getHeatmap(res, ...)

## S4 method for signature 'loci2pathResult'
getHeatmap(res, main = "",
  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
main	title of the heatmap, default is ""
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

pathways	frequent pathways
tissues	frequent tissues

Examples

result <- query(query.gr=query.gr, 
  loci=eset.list, path=biocarta)
getHeatmap(result)

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