I have an RleList I want to apply some functions on.

A small reprex of the object I need

IRanges::RleList(
  chr1 = 1:20,
  chr2 = 20:1
) -> cvg
GenomicRanges::GRanges(
  S4Vectors::Rle(c("chr1", "chr2"), c(2, 1)),
  IRanges::IRanges(c(1, 4, 2), width=c(4, 8, 6), names=head(letters, 3)),
  S4Vectors::Rle(GenomicRanges::strand(c("-", "+", "-")), c(1, 1, 1))
) -> gr

(v <- IRanges::Views(cvg, gr))

RleViewsList object of length 2:
$chr1
Views on a 20-length Rle subject

views:
    start end width
[1]     1   4     4 [1 2 3 4]
[2]     4  11     8 [ 4  5  6  7  8  9 10 11]

$chr2
Views on a 20-length Rle subject

views:
    start end width
[1]     2   7     6 [19 18 17 16 15 14]

On this object we would like to apply some functions, but I can't understand the behavior. Sometimes it returns an error I can't identify.

For once, the mean function doesn't work on the list ...

sapply(X = v, FUN = mean)

Warning in mean.default(x) :
  argument is not numeric or logical: returning NA
Warning in mean.default(x) :
  argument is not numeric or logical: returning NA
chr1 chr2 
  NA   NA

but the sum function does

sapply(X = v, FUN = sum)

$chr1
 a  b 
10 60 

$chr2
 c 
99

Any ideas why there is this difference?

The main difficulty I encounter is, that I try to bin the single elements within each of the lists inside the RleList object using the cut function

For that i have created a function

my_cut <- function(x) {
  cut(1:IRanges::width(x), 3)
}

But when I try to use the function, it only takes into account only the first element in each of the groups (hence the warning).

sapply(v, my_cut)

Warning in 1:IRanges::width(x) :
  numerical expression has 2 elements: only the first used
$chr1
[1] (0.997,2] (0.997,2] (2,3]     (3,4]    
Levels: (0.997,2] (2,3] (3,4]

$chr2
[1] (0.995,2.67] (0.995,2.67] (2.67,4.33]  (2.67,4.33]  (4.33,6]     (4.33,6]    
Levels: (0.995,2.67] (2.67,4.33] (4.33,6]

I would appreciate the help for this two problems/question

thanks in advance

Assa

Regarding the difference in behaviour between sum() and mean() I think this is because there is a sum() method defined for the RleViews class, which presumably knows how to handle it in a sensible fashion. However this is not true for mean(), and hence it doesn't perform as you're hoping.

> showMethods("sum")
Function: sum (package base)
x="CompressedIntegerList"
x="CompressedLogicalList"
x="CompressedNumericList"
x="Rle"
    (definition from function "Summary")
x="RleViews"
    (inherited from: x="Views")
    (definition from function "Summary")

> showMethods("mean")
Function "mean":
 <not an S4 generic function>

However you can make a reasonable stab at replicating the behaviour you see with sum() e.g.

lapply(v, FUN = function(x) {
    vapply(x, FUN = mean, FUN.VALUE = numeric(1))
})
# $chr1
#   a   b 
# 2.5 7.5 
#
# $chr2
#    c 
# 16.5

or you can use viewMeans() as Michael suggested. That's probably much more efficient if you're working on real data:

viewMeans(v)
# NumericList of length 2
# [["chr1"]] a=2.5 b=7.5
# [["chr2"]] c=16.5

I don't think I follow what you're trying to do with cut(). What's the expected output if it works as you intend?