prepInput {fedup} | R Documentation

## Prepares input gene list for runFedup.

### 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)

[Package fedup version 1.2.0 Index]