format_results {FGNet} | R Documentation

## Format FEA results from external tools.

### Description

Format the functional analysis results from external tools to use with FGNet.

### Usage

    format_results(fileName, newFileName = NULL, clusterCol = NULL,
        geneCol = NULL, geneSep = NULL, termDescCol = NULL, termIDCol = NULL,
        termCatCol = NULL, termCat = NULL, termSep = NULL,
        tool = "Imported text file", simplifyGage = TRUE, ...)

### Arguments

`fileName` | character. File name with the FEA results.
`newFileName` | character. Name for the formatted files.
`clusterCol` | character. Name of the column to use for clustering.
`geneCol` | character. Name of the column with the genes.
`geneSep` | character. Character separating diferent genes in the same field (i.e. ",", ";", ...)
`termDescCol` | character. Name of the column with the terms description.
`termIDCol` | character. Name of the column with the terms ID.
`termCatCol` | character. Name of the column with the terms type/category.
`termCat` | character. Name of the annotation type if it is common to all gene-term sets. Provide either termCatCol or termCat, not both.
`termSep` | character. Character separating diferent terms in the same field (i.e. ",", ";", ...)
`tool` | character. Tool used for the FEA (row name from `data(FEA_tools); FEA_tools`)
`simplifyGage` | logical. For internal use, only for GAGE. Determines wether to keep non essential terms in the final clusters.
`...` | Further argumets to pass to "read.table"

### Value

Saves the formatted file and returns an invisible list with the appropiate format to use with FGNet_report() and fea2incidMat() (fields "clusters", "geneTermSets" and "fileName").

### See Also

Overview of the package: `FGNet`

Package tutorial: `vignette("FGNet-vignette")`

### Examples

    ## Not run:

    results <- format_results("/home/user/feaResults.txt", clusterCol="Cluster",
        geneCol="Genes", termDescCol="Terms", sep="\t")

    ## End(Not run)

[Package FGNet version 3.22.1 Index]