[Bioc-devel] Bioc-devel changes and SummarizedExperiment class

[Leonard Goldstein]

Thanks Hervé!

Leonard


On Tue, Apr 10, 2018 at 11:03 AM, Hervé Pagès <hpages at fredhutch.org> wrote:

> Hi Leonard,
>
> This should be fixed in SGSeq 1.13.6 (see commit
> 5dc16968f7ea1a4b59595ebaabacca9a76699b80).
>
> Cheers,
> H.
>
>
> On 04/04/2018 09:23 AM, Leonard Goldstein wrote:
>
>> Hi Hervé,
>>
>> Some recent changes in bioc-devel are causing trouble with
>> SummarizedExperiment objects if the rowRanges slot inherits from
>> GRangesList. Please see example below.
>>
>> Thanks in advance for your help.
>>
>> Leonard
>>
>> --
>>
>>> library(SGSeq)
>>>
>>> ## SGVariants object inherits from GRangesList
>>>
>>
>>
>> is(sgv_pred)
>>>
>>   [1] "SGVariants"                         "GRangesList"
>>   [3] "Paths"                              "GenomicRangesList"
>>   [5] "CompressedRangesList"               "GenomicRanges_OR_GRangesList"
>>   [7] "RangesList"                         "CompressedList"
>>   [9] "GenomicRanges_OR_GenomicRangesList" "List"
>> [11] "Vector"                             "list_OR_List"
>> [13] "Annotated"
>>
>>>
>>> ## example counts
>>>
>>
>>
>> counts <- matrix(1:2, ncol = 1)
>>>
>>> ## creating SummarizedExperiment object fails
>>>
>>
>>
>> SummarizedExperiment(assays = list(counts), rowRanges = sgv_pred)
>>>
>> class: RangedSummarizedExperiment
>> dim: 2 1
>> metadata(0):
>> assays(1): ''
>> Error in .local(object, ..., verbose) : unused argument (check = FALSE)
>>
>>>
>>> ## works after coercing to GRangestList
>>>
>>
>>
>> SummarizedExperiment(assays = list(counts), rowRanges = as(sgv_pred,
>>>
>> "GRangesList"))
>> class: RangedSummarizedExperiment
>> dim: 2 1
>> metadata(0):
>> assays(1): ''
>> rownames: NULL
>> rowData names(20): from to ... variantType variantName
>> colnames: NULL
>> colData names(0):
>>
>>>
>>> sessionInfo()
>>>
>> R Under development (unstable) (2017-10-20 r73567)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago)
>>
>> Matrix products: default
>> BLAS:
>> /gnet/is2/p01/apps/R/3.5.0-20171105-devel/x86_64-linux-2.6-
>> rhel6/lib64/R/lib/libRblas.so
>> LAPACK:
>> /gnet/is2/p01/apps/R/3.5.0-20171105-devel/x86_64-linux-2.6-
>> rhel6/lib64/R/lib/libRlapack.so
>>
>> locale:
>>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats4    parallel  stats     graphics  grDevices utils     datasets
>> [8] methods   base
>>
>> other attached packages:
>>   [1] SGSeq_1.13.5                SummarizedExperiment_1.9.16
>>   [3] DelayedArray_0.5.23         BiocParallel_1.13.3
>>   [5] matrixStats_0.53.1          Biobase_2.39.2
>>   [7] Rsamtools_1.31.3            Biostrings_2.47.12
>>   [9] XVector_0.19.9              GenomicRanges_1.31.23
>> [11] GenomeInfoDb_1.15.5         IRanges_2.13.28
>> [13] S4Vectors_0.17.39           BiocGenerics_0.25.3
>>
>> loaded via a namespace (and not attached):
>>   [1] Rcpp_0.12.16              compiler_3.5.0
>>   [3] GenomicFeatures_1.31.10   prettyunits_1.0.2
>>   [5] bitops_1.0-6              tools_3.5.0
>>   [7] zlibbioc_1.25.0           progress_1.1.2
>>   [9] biomaRt_2.35.13           digest_0.6.15
>> [11] bit_1.1-13                RSQLite_2.1.0
>> [13] memoise_1.1.0             lattice_0.20-35
>> [15] pkgconfig_2.0.1           igraph_1.2.1
>> [17] Matrix_1.2-13             DBI_0.8
>> [19] GenomeInfoDbData_1.1.0    rtracklayer_1.39.9
>> [21] httr_1.3.1                stringr_1.3.0
>> [23] bit64_0.9-8               grid_3.5.0
>> [25] R6_2.2.2                  AnnotationDbi_1.41.4
>> [27] XML_3.98-1.10             blob_1.1.1
>> [29] magrittr_1.5              GenomicAlignments_1.15.13
>> [31] RUnit_0.4.31              assertthat_0.2.0
>> [33] stringi_1.1.7             RCurl_1.95-4.10
>>
>>>
>>>
>>>
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>>
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>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
>

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