getPval {loci2path} | R Documentation |
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
getPval(res, ...) ## S4 method for signature 'loci2pathResult' getPval(res, test.method = c("gene", "eqtl", "glm"))
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) |
generate pval distribution plot
result <- query(query.gr=query.gr, loci=eset.list, path=biocarta) getPval(result, test.method="gene")