Format FEA results from external tools.

Share:

Description

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

Usage

1
2
3
4
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

1
2
3
4
5
6
7
## Not run: 

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


## End(Not run)