format_results {FGNet} | R Documentation |
Format the functional analysis results from external tools to use with FGNet.
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, ...)
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 |
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" |
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").
Overview of the package: FGNet
Package tutorial: vignette("FGNet-vignette")
## Not run: results <- format_results("/home/user/feaResults.txt", clusterCol="Cluster", geneCol="Genes", termDescCol="Terms", sep="\t") ## End(Not run)