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

[Hervé Pagès]

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
>>
>>
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=qpgk0XNxCYLZKHMRS-PnHD2znDDwj1P-Eiu7P4aUSuI&s=qjwH7TgvfYKGtMDCI77_VVUw8S-5PA6ctju8Jb3erUQ&e=
> 

-- 
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