prepInput: Prepares input gene list for runFedup.

In rosscm/fedup: Fisher's Test for Enrichment and Depletion of User-Defined Pathways

Description

This function takes any number of test genes and a common background set of genes and properly formats them for to pass to runFedup gene argument.

Usage

prepInput(setName, ...)

Arguments

setName	(char) character vector naming gene vectors passed to ... (must include "background" (case sensitive)).
...	(char) n vectors with at least one background set of genes and any number of test genes.

Value

List of length n with gene vectors corresponding to those passed to ....

Examples

# Raw gene data file
genesFile <- system.file("extdata",
    "NIHMS1587165-supplement-1587165_Sup_Tab_2.txt", package = "fedup")
genes <- read.delim(genesFile, h = TRUE, as.is = TRUE)
# Prepare gene vectors
b <- unique(genes[, "gene"])
set1 <- unique(genes[which(genes$FASN_merge < -0.4), "gene"])
set2 <- unique(genes[which(genes$FASN_merge > 0.4), "gene"])
setName <- c("background", "negative", "positive")
# Generate input list with background genes and two test set of genes
geneDouble <- prepInput(setName, b, set1, set2)

rosscm/fedup documentation built on July 19, 2021, 2:21 a.m.