Nothing
# fileName <- "goResTable.txt"
readGeneTermSets <- function(fileName, tool=NULL, simplifyGage=TRUE)
{
data("FEA_tools", envir = environment())
FEA_tools<- get("FEA_tools", envir = environment())
# Read file
sepChar <- "\t"
geneTermSets <- read.table(fileName, sep=sepChar, header=TRUE, quote="")
if(any(is.na(geneTermSets$Genes)) || ("GenesIDs" %in% colnames(geneTermSets) && any(is.na(geneTermSets$GenesIDs))))
{
warning("Some gene-term sets contain no genes.")
geneTermSets$Genes[is.na(geneTermSets$Genes)] <- ""
if("GenesIDs" %in% colnames(geneTermSets)) geneTermSets$GenesIDs[is.na(geneTermSets$GenesIDs)] <- ""
}
# Create clusters table
colsAvg <- NULL
sortBy <- NULL
if(!is.null(tool))
{
colsAvg <- sortBy <- FEA_tools[tool,"DefaultFilter"]
if(is.na(colsAvg)) colsAvg <- sortBy <- NULL
}
if(!is.null(tool) && tool=="gage")
{
# gage:
keepTermsCol <- NULL
if(simplifyGage) keepTermsCol <- "essentialSet"
tablaClusters <- clustersTable(geneTermSets, colsAvg="dir", sortBy=NULL, keepTermsCol=keepTermsCol, addKeyWordsTerm=FALSE)
}else
{
# Default, any other case
tablaClusters <- clustersTable(geneTermSets, colsAvg=colsAvg, sortBy=sortBy, decreasing=TRUE) # keepTermsCol=NULL, addKeyWordsTerm=TRUE,
}
# Return
invisible(list(clusters=tablaClusters, geneTermSets=geneTermSets, fileName=fileName))
}
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