This is fixed in 1.10.8 of biovizBase. That function was totally broken.
Consider it deprecated.


On Thu, Feb 27, 2014 at 9:29 PM, Michael Lawrence <michafla@gene.com> wrote:

> I'll fix this in the morning, but I wanted to note that pileupVariants in
> the devel VariantTools is a lot more efficient and outputs a more
> appropriate VRanges object. I just need to find a way to make VariantTools
> optionally dependent on gmapR, so that it can be installed on Windows.
>
>
> On Thu, Feb 27, 2014 at 5:33 PM, Katherine Yahvah <kyahvah@novuscmd.com>wrote:
>
>> Hello-
>> I'm running into an almost identical problem that was previously posted (
>> https://stat.ethz.ch/pipermail/bioconductor/2013-March/051793.html ) but
>> have not found a solution to make the analysis work.
>>
>> I am trying to use pileupAsGRanges to generate the base counts at each
>> nucleotide position in a GRanges object.  My GRanges object:
>> > gr
>> GRanges with 225 ranges and 1 metadata column:
>>         seqnames               ranges strand   |   seqinfo
>>            <Rle>            <IRanges>  <Rle>   | <integer>
>>     [1]     chr1 [ 4367322,  4367323]      *   |         1
>>     [2]     chr1 [14155401, 14155402]      *   |         2
>>     [3]     chr1 [14996653, 14996654]      *   |         3
>>     [4]     chr1 [34155500, 34155501]      *   |         4
>>     [5]     chr1 [54195017, 54195018]      *   |         5
>>     ...      ...                  ...    ... ...       ...
>>   [221]    chr22 [43579707, 43579708]      *   |       221
>>   [222]    chr22 [47836411, 47836412]      *   |       222
>>   [223]    chr22 [48362289, 48362290]      *   |       223
>>   [224]     chrY [ 8619537,  8619538]      *   |       224
>>   [225]     chrY [14096576, 14096577]      *   |       225
>>   ---
>>   seqlengths:
>>     chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19  chr2
>> chr20 chr21 chr22  chr3  chr4  chr5  chr6  chr7  chr8  chr9  chrY
>>       NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA
>> NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA
>>
>>
>> However, when I try to run pileupAsGRanges I get an error:
>>
>> >
>>
>> test<-pileupAsGRanges(bam=fls,regions=gr,maxDepth=.Machine$integer.max,minBa
>> seQuality=30, minMapQuality=30)
>> Error: applyPileups: invalid 'times' argument
>> In addition: Warning messages:
>> 1: In start(regions):end(regions) :
>>   numerical expression has 225 elements: only the first used
>> 2: In start(regions):end(regions) :
>>   numerical expression has 225 elements: only the first used
>>
>> If I run the command with only one element of the GRanges object the
>> function works:
>>
>> >
>>
>> test<-pileupAsGRanges(bam=fls,regions=gr[1],maxDepth=.Machine$integer.max,mi
>> nBaseQuality=30, minMapQuality=30)
>> > test
>> GRanges with 2 ranges and 7 metadata columns:
>>       seqnames             ranges strand |         A         C         G
>> T         N     depth                        bam
>>          <Rle>          <IRanges>  <Rle> | <integer> <integer> <integer>
>> <integer> <integer> <numeric>                <character>
>>   [1]     chr1 [4367322, 4367322]      + |       233         0         1
>> 0         0       234 ./IonXpress_001_rawlib.bam
>>   [2]     chr1 [4367323, 4367323]      + |       467         0         0
>> 0         0       467 ./IonXpress_001_rawlib.bam
>>   ---
>>   seqlengths:
>>    chr1
>>      NA
>>
>> Any help to figure out how to correct or work around this problem would be
>> greatly appreciated.
>> Regards,
>> Katherine Yahvah
>> Research Scientist
>> Kashi Clinical Laboratories
>> Portland, OR
>>
>> > sessionInfo()
>> R version 3.0.2 (2013-09-25)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>>
>> locale:
>> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
>> States.1252    LC_MONETARY=English_United States.1252
>> [4] LC_NUMERIC=C                           LC_TIME=English_United
>> States.1252
>>
>> attached base packages:
>> [1] grid      parallel  stats     graphics  grDevices utils     datasets
>> methods   base
>>
>> other attached packages:
>>  [1] BSgenome.Hsapiens.UCSC.hg19_1.3.19  ChIPpeakAnno_2.10.0
>> GenomicFeatures_1.14.3
>>  [4] limma_3.18.13                       org.Hs.eg.db_2.10.1
>> GO.db_2.10.1
>>  [7] RSQLite_0.11.4                      DBI_0.2-7
>> AnnotationDbi_1.24.0
>> [10] BSgenome.Ecoli.NCBI.20080805_1.3.17 BSgenome_1.30.0
>> multtest_2.18.0
>> [13] Biobase_2.22.0                      biomaRt_2.18.0
>> VennDiagram_1.6.5
>> [16] Rsamtools_1.14.3                    Biostrings_2.30.1
>> biovizBase_1.10.7
>> [19] BiocInstaller_1.12.0                GenomicRanges_1.14.4
>> XVector_0.2.0
>> [22] IRanges_1.20.6                      BiocGenerics_0.8.0
>>
>> loaded via a namespace (and not attached):
>>  [1] bitops_1.0-6        cluster_1.14.4      colorspace_1.2-4
>> dichromat_2.0-0     Formula_1.1-1       Hmisc_3.14-1        labeling_0.2
>>
>>  [8] lattice_0.20-24     latticeExtra_0.6-26 MASS_7.3-29
>> munsell_0.4.2       plyr_1.8            RColorBrewer_1.0-5  RCurl_1.95-4.1
>>
>> [15] rtracklayer_1.22.3  scales_0.2.3        splines_3.0.2
>> stats4_3.0.2        stringr_0.6.2       survival_2.37-7     tools_3.0.2
>>
>> [22] XML_3.98-1.1        zlibbioc_1.8.0
>>
>> _______________________________________________
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>>
>
>

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