run_spia: Prepare gene lists and run spia

In mworkentine/mattsUtils: Personal Utility Functions For Various Analysis

Description

Wrapper for graphite::runSPIA. Will save the database file in the current working directory if not already present. Does some prep work with gene ids and cleans up the output a bit. Only supports reactome and kegg for now.

Usage

run_spia(res, dds, organism, database = c("reactome", "kegg"),
  key = NULL, cutoff = 0.05)

Arguments

res	data frame with the columns 'estimate' and 'gene. Usually DESeq results processed with biobroom::tidy
dds	valid DESeq object from which the results were generated
organism	character, the organism to use. See available organisms with pathwayDatabases()
database	character, the pathway database to use, one of c("reactome", "kegg").
key	named character vector to use for converting gene IDs to Entrez IDs if needed
cutoff	numeric, p-value cutoff

Value

same as runSPIA but cleaned up, with database links added and pathways filtered to the privided cutoff

mworkentine/mattsUtils documentation built on May 23, 2019, 11:58 a.m.