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@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: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
