getHeatmap {loci2path} | R Documentation |
This function generate the enrichment heatmap using pheatmap package.
getHeatmap(res, ...) ## S4 method for signature 'loci2pathResult' getHeatmap(res, main = "", test.method = c("gene", "eqtl", "glm"), filter.quantile = 0.5, max.ptw.gene = 5000)
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) |
pathways |
frequent pathways |
tissues |
frequent tissues |
result <- query(query.gr=query.gr, loci=eset.list, path=biocarta) getHeatmap(result)