Hi :

I have list of position index in the IntegerList, and I intended to filter them given threshold, and it works well. However, I want to extract out one of specific filtered set for each IntegerList for further usage. I aware that myList is nested list , and data are very much simulated based on real data set. Is there any way to retrieve wanted IntegerList easily and elegantly? How can I make it this extraction happen? 

mini example :

myList <- list(f1=IntegerList(1,2,3,4,1,1,1,integer(0),1,2,4),
               f2=IntegerList(1,5,integer(0),integer(0),2,3,4,6,1,5,6),
               f3=IntegerList(1,4,6,7,2,3,3,7,2,5,7))

len <- Reduce('+', lapply(myList, lengths))
keepMe <- len >= length(myList)

I did following filtering: 

res.filt <- lapply(myList, function(elm) {
  ans <- list(keep=elm[keepMe], droped=elm[!keepMe])
  ans
})

my rough attempt output :

wantedKeep.list <- list(f1.kp=res.filt$f1$keep, f2.kp=res.filt$f2$keep, f3.kp=res.filt$f3$keep)
wantedDrop.list <- list(f1.dp=res.filt$f1$droped, f2.dp=res.filt$f2$droped, f3.dp=res.filt$f3$droped)

Based on my rough output, How can I get more elegant output ? any efficient way to achieve my output ? Can anyone point me how to do? Or any suggestion how to get my expected output ?  Thanks in advance

It looks like you are thnking of the data as a matrix. You can create a list matrix like this:

v <- unlist(lapply(myList, as.list), recursive=FALSE)
m <- matrix(v, length(myList), byrow=TRUE)
rownames(m) <- names(myList)

Then you can compute lengths and make the selection:

lens <- lengths(m)
dim(lens) <- dim(m)
keep <- colSums(lens) >= nrow(m)
keepList <- m[,keep,drop=FALSE]
dropList <- m[,!keep,drop=FALSE]

I will work on making some of these operations easier. But it's pretty straight-forward as is.

Is it the case that all of the elements are of length either 1 or 0? If so, it might be easier to convert the zero-length elements to NAs and drop to a vector.

Here is a simpler solution in Bioc devel for generating the matrix "m" (first three lines above):

m <- do.call(rbind, myList)

Also, I will push a change to R devel so that lengths() preserves matrix dimensions, so they do not need to be carried over.