ksRepo: ksRepo

In adam-sam-brown/ksRepo: ksRepo - a Generalized Platform for Computational Drug Repositioning

Description

ksRepo performs KS-based repositioning of user supplied data. KS values are assigned p-values by bootstrapping the user supplied datasets.

Usage

ksRepo(ccgenes, database, boot.method = "compound", nboot = 10000)

Arguments

ccgenes	A character vector of prioritized genes derived from a case/control dataset. Examples include differential gene expression, differential methylation, and mutation frequency.
database	A named list object representing a gene::compound interaction database. List items should be named with compound names and their contents should be interacting genes.
boot.method	A string specifying whether the 'compound' gene lists or the case/control, 'instance' dataset should be permuted for bootstrapping. Default is to permute the compound gene lists.
nboot	An integer specifying the number of bootstrap samples for p-value calculation.

Value

A data frame with C rows and 5 columns, where C is the number of compounds in the database. compound gives name of the compound. n.genes gives the number of genes associated with each compound. ks gives the raw ks statistic, boot.p gives the bootstrapped p-value, and boot.fdr gives the fdr-corrected bootstrapped p-value.

adam-sam-brown/ksRepo documentation built on May 10, 2019, 5:13 a.m.