Hi Leonard,
Sorry for missing your earlier posts about this. Will look into it.
Thanks,
H.
On 10/27/2017 09:07 AM, Leonard Goldstein wrote:
Dear bioc-devel,
I noticed exonsBy is dropping a lot of genes when run on a TxDb object
created with makeTxDbFromBiomart (see below). Please also see related post
on the Bioconductor support site:
https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_101951_-23102160&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ExVvVr6r4wUKgBmPNOQiJXSI2O1FYqFRz_llKQY_jD0&s=xUz41e2CIjMTXmO5LqkFp12ySvH9zzA0s5OMWzgWosU&e=
Thanks for your help.
Leonard
--
tx <- makeTxDbFromBiomart()
txs_by_gene <- transcriptsBy(tx, "gene")
exs_by_gene <- exonsBy(tx, "gene")
length(txs_by_gene)
[1] 63967
length(exs_by_gene)
[1] 36751
subsetByOverlaps(txs_by_gene, GRanges("8", IRanges(127735434,127741434)))
GRangesList object of length 1:
$ENSG00000136997
GRanges object with 9 ranges and 2 metadata columns:
seqnames ranges strand | tx_id tx_name
<Rle> <IRanges> <Rle> | <integer> <character>
[1] 8 [127735434, 127740477] + | 101876 ENST00000259523
[2] 8 [127735473, 127735817] + | 101877 ENST00000641252
[3] 8 [127735519, 127738772] + | 101878 ENST00000517291
[4] 8 [127736046, 127736612] + | 101879 ENST00000641036
[5] 8 [127736069, 127741434] + | 101880 ENST00000621592
[6] 8 [127736084, 127741434] + | 101881 ENST00000377970
[7] 8 [127736220, 127741372] + | 101882 ENST00000524013
[8] 8 [127736231, 127738475] + | 101883 ENST00000520751
[9] 8 [127736594, 127740958] + | 101884 ENST00000613283
-------
seqinfo: 555 sequences (1 circular) from an unspecified genome
subsetByOverlaps(exs_by_gene, GRanges("8", IRanges(127735434,127741434)))
GRangesList object of length 0:
<0 elements>
-------
seqinfo: 555 sequences (1 circular) from an unspecified genome
sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6
Matrix products: default
BLAS:
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] GenomicFeatures_1.28.5 AnnotationDbi_1.38.2 Biobase_2.36.2
[4] GenomicRanges_1.28.6 GenomeInfoDb_1.12.3 IRanges_2.10.5
[7] S4Vectors_0.14.7 BiocGenerics_0.22.1
loaded via a namespace (and not attached):
[1] Rcpp_0.12.13 XVector_0.16.0
[3] GenomicAlignments_1.12.2 zlibbioc_1.22.0
[5] BiocParallel_1.10.1 bit_1.1-12
[7] lattice_0.20-35 rlang_0.1.2
[9] blob_1.1.0 tools_3.4.1
[11] grid_3.4.1 SummarizedExperiment_1.6.5
[13] DBI_0.7 matrixStats_0.52.2
[15] bit64_0.9-7 digest_0.6.12
[17] tibble_1.3.4 Matrix_1.2-11
[19] GenomeInfoDbData_0.99.0 rtracklayer_1.36.6
[21] bitops_1.0-6 RCurl_1.95-4.8
[23] biomaRt_2.32.1 memoise_1.1.0
[25] RSQLite_2.0 DelayedArray_0.2.7
[27] compiler_3.4.1 Rsamtools_1.28.0
[29] Biostrings_2.44.2 XML_3.98-1.9
[31] pkgconfig_2.0.1
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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: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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