Nothing
calcCombVals <-
function(data,groupID,colID="FPKM",combineCols=TRUE,
matchEnd=TRUE,FUN="mean",functionName=NULL){
## groupID should either me vector of characters defining group,
## or a list of the column's for each group (e.g. list(Vfpkm=c(1,2,3),Cfpkm=(4,5,6)))
## If using characters make sure the names are unique enough to match only what you want them to
## data should be matrix or data.frame
## colID tells which measure you want the mean of, can be a vector for several things
## combineCols tells whether or not to put the colums into one data.frame
## FUN should either be a function or a character to match to function
## If not a character, set functionName to assign column names for the output
## Name the function Set which function to use:
if(is.null(functionName)){
functionName <- as.character(FUN )
}
FUN<-match.fun(FUN)
colIndex <- list() # set a variable to hold the column index
if(is.character(groupID)){
for(j in 1:length(colID)){
## Set colID to "*" for searching, if it is blank
if(colID[j]==""|colID[j]=="*"|colID[j]=="all"){
colID[j]<-"*"
colName <- "all"
} else{
colName <- colID[j]
}
indCols <- character()
for(k in 1:length(groupID)){
## set groupID to "*" if blank, to match all instead of none
if(groupID[k]==""|groupID[k]=="*"){
groupID[k]<-"*"
groupName <- "all"
}else{
groupName <- groupID[k]
}
if(matchEnd){
indCols <- c(indCols,grep(paste(colID[j],"$",sep=""),colnames(data),value=TRUE) )
} else {
indCols <- grep(colID[j],colnames(data),value=TRUE)
}
colIndex[[paste(groupName,colName,functionName,sep="_")]] <- grep(groupID[k],indCols,value=TRUE)
}
}
} else if(is.list(groupID)) {
colIndex <- groupID
} else {
stop("ERROR: colID must be either numeric or character")
}
temp <- lapply(colIndex,function(x) {apply(data[,x],1,FUN)})
if(combineCols){
tempOut <- as.data.frame(do.call(cbind,temp) )
} else{
tempOut <- temp
}
return(tempOut)
}
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