[Bioc-devel] asVCF error coming from normalizeSingleBracketSubscript

[Hervé Pagès]

Hi Val, Stephanie,

I wonder what's the purpose of comparing a NumericList with the
empty string in the first place. That's always going to return a
LogicalList filled with FALSEs. So x[x %in% ""] <- NA is always
going to be a no-op. There might be a deeper issue with this code.

Cheers,
H.


On 11/25/2013 02:08 PM, Valerie Obenchain wrote:
> 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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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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