format_results: Format FEA results from external tools.

In FGNet: Functional Gene Networks derived from biological enrichment analyses

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)

FGNet documentation built on Nov. 8, 2020, 5:43 p.m.