Hi Stephanie,
The error is thrown from SeqArray:::.info at line 216 in the file and is
related to the handing of NA values.
x[x == ""] <- NA
Output from the == comparison can contain NAs and therefore can't be
used (consistently) in subsetting operations.
'x' is a NumericList.
Browse[2]> x
NumericList of length 5
[[1]] 0.5
[[2]] 0.017000000923872
[[3]] 0.333000004291534 0.666999995708466
[[4]] <NA>
[[5]] <NA> <NA>
Here we see NAs returned for the NA values,
Browse[2]> x == ""
LogicalList of length 5
[[1]] FALSE
[[2]] FALSE
[[3]] FALSE FALSE
[[4]] <NA>
[[5]] <NA> <NA>
which fail on subsetting.
Browse[2]> x[x == ""]
Error in normalizeSingleBracketSubscript(i, x) : subscript contains NAs
One solution is use %in% which does not return NAs.
Browse[2]> x %in% ""
LogicalList of length 5
[[1]] FALSE
[[2]] FALSE
[[3]] FALSE FALSE
[[4]] FALSE
[[5]] FALSE FALSE
Valerie
On 11/22/2013 03:11 PM, Stephanie M. Gogarten wrote:
Hi Valerie,
The asVCF method in SeqArray is failing as of today with a (to me)
mysterious error. I get it for the test files chr22.vcf.gz, ex2.vcf,
and gl_chr1.vcf in extdata of VariantAnnotation, but not for
SeqArray/extdata/CEU_Exon.vcf. Do you have any suggestions of where I
might look to figure out where this error is coming from?
thanks,
Stephanie
> vcffile <- system.file("extdata", "ex2.vcf",
package="VariantAnnotation")
> gdsfile <- tempfile()
> seqVCF2GDS(vcffile, gdsfile)
> gdsobj <- seqOpen(gdsfile)
> options(error=recover)
> vcfg <- asVCF(gdsobj)
Error in normalizeSingleBracketSubscript(i, x) : subscript contains NAs
Enter a frame number, or 0 to exit
1: asVCF(gdsobj)
2: asVCF(gdsobj)
3: .local(x, ...)
4: VCF(rowData = .rowData(x), colData = .colData(x), exptData =
SimpleList(hea
5: .info(x, info)
6: `[<-`(`*tmp*`, x == "", value = NA)
7: `[<-`(`*tmp*`, x == "", value = NA)
8: lsubset_List_by_List(x, i, value)
9: .fast_lsubset_List_by_List(x, i, value)
10: replaceROWS(unlisted_x, unlisted_i, unlisted_value)
11: replaceROWS(unlisted_x, unlisted_i, unlisted_value)
12: extractROWS(setNames(seq_along(x), names(x)), i)
13: extractROWS(setNames(seq_along(x), names(x)), i)
14: normalizeSingleBracketSubscript(i, x)
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] VariantAnnotation_1.8.6 Rsamtools_1.14.1 Biostrings_2.30.1
[4] GenomicRanges_1.14.3 XVector_0.2.0 IRanges_1.20.6
[7] BiocGenerics_0.8.0 SeqArray_1.2.0 gdsfmt_1.0.0
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.24.0 Biobase_2.22.0 biomaRt_2.18.0
[4] bitops_1.0-6 BSgenome_1.30.0 DBI_0.2-7
[7] GenomicFeatures_1.14.2 RCurl_1.95-4.1 RSQLite_0.11.4
[10] rtracklayer_1.22.0 stats4_3.0.2 tools_3.0.2
[13] XML_3.95-0.2 zlibbioc_1.8.0
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