It seems that there is diversity in the classes assigned for ALT in results
of readVcf, and there was some discussion of this in 1/2013. So it looks
like this is predictable and solvable with some upstream work after the
read.
On Sun, Mar 16, 2014 at 7:43 PM, Vincent Carey
<st...@channing.harvard.edu>wrote:
> > 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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