run_druid: Run DRUID

In diogocamacho/druid: Drug Indication Discoverer

Description

Given a selection on the drug compendium, produces a data frame with the results of DRUID. Makes the 'concoct' function somewhat redundant (to be revised later.)

Usage

run_druid(dge_matrix, druid_direction, fold_thr, pvalue_thr, entrez,
  num_random, selection)

Arguments

dge_matrix	This is a 2 column matrix for gene expression changes, where column 1 is the gene fold change and column 2 is the corresponding p-value for the fold change. NOTE: Use log2 of the fold changes as output, for example, from 'limma' or 'DESeq2'.
druid_direction	Desired effect for DRUID to run on: "pos" mimics query phenotype, "neg" reverts query phenotype. Defaults to "neg".
fold_thr	Threshold for the fold change to be considered. Defaults to 0 (i.e., log2(1), where fold change is not used as filter)
pvalue_thr	Threshold for the p-value of the fold change to be considered. Defaults to 0.05.
entrez	EntrezIDs for genes in differentially expressed set. Must be same order as the input matrix.
num_random	Number of random sets to be generated to calculate significance of enrichment. Defaults to 1,000.
selection	EntrezIDs for genes in differentially expressed set. Must be same order as the input matrix.
tfidf_matrix	tf-idf matrix drug-gene matrix. Column names are Entrez IDs. Computed with ctfidf

Value

A data frame that is sorted on the DRUID score.

diogocamacho/druid documentation built on Sept. 17, 2020, 12:39 p.m.