Hi Vince,
ALT is a CharacterList when the variants are 'structural', i.e., when
the ALT field has non-nucleotide characters. Otherwise, ALT is a
DNAStringSetList.
It looks like ALT is a CharacterList in x[[1]] and is probably a
DNAStringSetList in x[[3]]. So you are trying to combine GRanges with
these two different types in ALT:
gr1 <- GRanges("1", IRanges(1:3, width=1),
ALT = CharacterList(list("A", "G", "A")))
gr2 <- GRanges("1", IRanges(5:7, width=1),
ALT = DNAStringSetList(list("T", "A", "C")))
c(gr1, gr2)
Error in .Primitive("c")(<S4 object of class "CompressedCharacterList">, :
all arguments in '...' must have an element class that extends that of the
first argument
The ALT values in the subset of x[[1]] are all nucleotides but not all
ALT values in x[[1]] are which is why readVcf() made it a CharacterList.
To combine these GRanges you need to either coerce all of x[[3]] ALT to
CharacterList or coerce the subset of x[[1]] to DNAStringSetList.
Coerce the subset of x[[1]] to DNAStringSetList:
gr1$ALT <- DNAStringSetList(gr1$ALT)
gr1
GRanges with 3 ranges and 1 metadata column:
seqnames ranges strand | ALT
<Rle> <IRanges> <Rle> | <DNAStringSetList>
[1] 1 [1, 1] * | A
[2] 1 [2, 2] * | G
[3] 1 [3, 3] * | A
---
Combine:
c(gr1, gr2)
GRanges with 6 ranges and 1 metadata column:
seqnames ranges strand | ALT
<Rle> <IRanges> <Rle> | <DNAStringSetList>
[1] 1 [1, 1] * | A
[2] 1 [2, 2] * | G
[3] 1 [3, 3] * | A
[4] 1 [5, 5] * | T
[5] 1 [6, 6] * | A
[6] 1 [7, 7] * | C
Val
On 03/16/2014 06:11 PM, Vincent Carey wrote:
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
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Valerie Obenchain
Program in Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B155
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: voben...@fhcrc.org
Phone: (206) 667-3158
Fax: (206) 667-1319
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
