> c(x[[1]][1:3,1:2], x[[3]][1:3,1:2])  # this works
GRanges with 6 ranges and 2 metadata columns:
      seqnames           ranges strand |    paramRangeID            REF
         <Rle>        <IRanges>  <Rle> |        <factor> <DNAStringSet>
  [1]        1 [ 10583,  10583]      * |  dhs_chr1_10402              G
  [2]        1 [ 10611,  10611]      * |  dhs_chr1_10402              C
  [3]        1 [ 10583,  10583]      * |  dhs_chr1_10502              G
  [4]        1 [832178, 832178]      * | dhs_chr1_833139              A
  [5]        1 [832266, 832266]      * | dhs_chr1_833139              G
  [6]        1 [832297, 832299]      * | dhs_chr1_833139            CTG
  ---
  seqlengths:
    1
   NA
> x[[1]][1:3,1:3]
GRanges with 3 ranges and 3 metadata columns:
      seqnames         ranges strand |   paramRangeID            REF
         <Rle>      <IRanges>  <Rle> |       <factor> <DNAStringSet>
  [1]        1 [10583, 10583]      * | dhs_chr1_10402              G
  [2]        1 [10611, 10611]      * | dhs_chr1_10402              C
  [3]        1 [10583, 10583]      * | dhs_chr1_10502              G
                  ALT
      <CharacterList>
  [1]               A
  [2]               G
  [3]               A
  ---
  seqlengths:
    1
   NA
> c(x[[1]][1:3,1:3], x[[3]][1:3,1:3])  # if i try to concatenate while ALT
is included
Error in .Primitive("c")(<S4 object of class "CompressedCharacterList">,  :
  all arguments in '...' must have an element class that extends that of
the first argument

Enter a frame number, or 0 to exit

 1: c(x[[1]][1:3, 1:3], x[[3]][1:3, 1:3])
 2: c(x[[1]][1:3, 1:3], x[[3]][1:3, 1:3])
 3: .local(x, ..., recursive = recursive)
 4: .unlist_list_of_GenomicRanges(args, ignore.mcols = ignore.mcols)
 5: do.call(rbind, lapply(x, mcols, FALSE))
 6: do.call(rbind, lapply(x, mcols, FALSE))
 7: (function (..., deparse.level = 1)
standardGeneric("rbind"))(<S4 object of
 8: standardGeneric("rbind")
 9: eval(.dotsCall, env)
10: eval(.dotsCall, env)
11: eval(expr, envir, enclos)
12: .Method(..., deparse.level = deparse.level)
13: lapply(seq_len(length(df)), function(i) {
    cols <- lapply(args, `[[`, cn[
14: lapply(seq_len(length(df)), function(i) {
    cols <- lapply(args, `[[`, cn[
15: FUN(1:3[[3]], ...)
16: do.call(c, unname(cols))
17: do.call(c, unname(cols))
18: .Primitive("c")(<S4 object of class "CompressedCharacterList">, <S4
object
19: .Primitive("c")(<S4 object of class "CompressedCharacterList">, <S4
object

> sessionInfo()
R Under development (unstable) (2014-03-15 r65199)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] parallel  stats     graphics  grDevices datasets  utils     tools
[8] methods   base

other attached packages:
 [1] Biostrings_2.31.14    XVector_0.3.7         GenomicRanges_1.15.39
 [4] GenomeInfoDb_0.99.19  IRanges_1.21.34       BiocGenerics_0.9.3
 [7] BatchJobs_1.2         BBmisc_1.5            weaver_1.29.1
[10] codetools_0.2-8       digest_0.6.4          BiocInstaller_1.13.3

loaded via a namespace (and not attached):
[1] DBI_0.2-7       RSQLite_0.11.4  Rcpp_0.11.1     brew_1.0-6
[5] fail_1.2        plyr_1.8.1      sendmailR_1.1-2 stats4_3.2.0
[9] stringr_0.6.2

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