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

[Leonard Goldstein]

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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