Hi everyone:

I have list of overlap hit index in IntegerList where some duplicated index exist. I have tried of using unique, or duplicated method from IRanges packages, but duplication can't be removed anyway. Removing duplication for GRanges object is different from IntegerList. However, I tried other way like such as coercing IntegerList to integer vector then use unique, or duplicated method, but if I do this way I could have NA instead (NA shouldn't be in IntegerList). Because I expect to have new IntegerList without duplicated index at the end. I think there might have other approach to accomplish task easily and efficiently . Can anyone propose any idea to accomplish this manipulation easily ? How can I make this happen ? 

updated mini example:

hitTB_1 <- list(
  foo = IntegerList(1,3,7,10),
  bar = IntegerList(1,3,integer(0),8),
  cat = IntegerList(1,3,integer(0),10)
)

hitTB_2 <- list(
  bar = IntegerList(1,4,8,9,10),
  foo = IntegerList(1,4,10,11,integer(0)),
  cat = IntegerList(1,4,10,13,14)
)

hitTB_3 <- list(
  cat = IntegerList(2,5,7,9,10),
  foo = IntegerList(2,5,8,integer(0),10),
  bar = IntegerList(2,5,7,integer(0),8)
)

So, each hitTB, order of IntegerList is different, I intend to manipulate them as follows:

idx <-  names(hitTB_1)
hitTB_1
hitTB_2 <- DataFrame(hitTB_2[idx])
hitTB_3 <- DataFrame(hitTB_3[idx])

So I could have same pattern with hitTB_1, and it is easier to combine them into one single list without duplication if it is feasible for doing this way. Any recommendation ?

If I could manipulate them as matrix, then I could get this output as my desired output.

desired output :

output <-
  DataFrame(
    foo = IntegerList(integer(0),integer(0),1,2,3,4,5,7,8,10,11),
    bar = IntegerList(integer(0),10,1,2,3,4,5,integer(0),7,8,9),
    cat = IntegerList(9,14,1,2,3,4,5,integer(0),7,10,13)
  )

I am stuck with this problem. How can I achieve my expected output easily? Any idea, possible approach are highly appreciated. Thanks a lot.

Best regards:

Jurat

Hi Jurat,

Are you getting the list of IntegerLists as the output from a function or are you creating it? If you are constructing it yourself it would be much easier to manipulate in a single IntegerList with NAs:

> hitTB <- IntegerList(
+   hit.1= c(1,2,3,NA,4,NA,NA,6),
+   hit.2 = c(1,1,1,2,NA,3,4,NA),
+   hit.3 = c(1,2,4,4,5,NA,6,7)
+ )
> hitTB
IntegerList of length 3
[["hit.1"]] 1 2 3 <NA> 4 <NA> <NA> 6
[["hit.2"]] 1 1 1 2 <NA> 3 4 <NA>
[["hit.3"]] 1 2 4 4 5 <NA> 6 7

unique() gives the desired result (if NAs are ok):
> unique(hitTB)
IntegerList of length 3
[["hit.1"]] 1 2 3 <NA> 4 6
[["hit.2"]] 1 2 <NA> 3 4
[["hit.3"]] 1 2 4 5 <NA> 6 7

I didn't quite follow your rational of NA values. Do you not want them in the final list?

Valerie