Hi Robert, I'm working on this.
Best, H. On 07/14/2017 02:31 AM, Robert Castelo wrote:
hi, the strand replacement method for 'GPos' objects does not seem to work: library(GenomicRanges) example(GPos) strand(gpos1) <- "-" Error in methods::slot(object, name) : no slot of name "call" for this object of class "GPos" traceback() 10: methods::slot(object, name) 9: getElement(x, "call") 8: getCall.default(object) 7: getCall(object) 6: update.default(x, strand = value, check = FALSE) 5: update(x, strand = value, check = FALSE) 4: update(x, strand = value, check = FALSE) 3: .local(x, ..., value) 2: `strand<-`(`*tmp*`, value = "-") 1: `strand<-`(`*tmp*`, value = "-") this kind of operation works perfectly on 'GRanges' objects, so i guess it should also work also with 'GPos' objects: example(GRanges) gr1 GRanges object with 1 range and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> <Rle> [1] chr2 [56, 125] * ------- seqinfo: 1 sequence from an unspecified genome; no seqlength strand(gr1) <- "-" gr1 GRanges object with 1 range and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> <Rle> [1] chr2 [56, 125] - ------- seqinfo: 1 sequence from an unspecified genome; no seqlengths below my session info. thanks! robert. ps: sessionInfo() sessionInfo() R version 3.4.0 (2017-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS: /opt/R/R-3.4.0/lib64/R/lib/libRblas.so LAPACK: /opt/R/R-3.4.0/lib64/R/lib/libRlapack.so locale: [1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF8 LC_COLLATE=en_US.UTF8 [5] LC_MONETARY=en_US.UTF8 LC_MESSAGES=en_US.UTF8 [7] LC_PAPER=en_US.UTF8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] GenomicRanges_1.28.3 GenomeInfoDb_1.12.2 IRanges_2.10.2 [4] S4Vectors_0.14.3 BiocGenerics_0.22.0 colorout_1.1-2 loaded via a namespace (and not attached): [1] zlibbioc_1.22.0 compiler_3.4.0 tools_3.4.0 [4] XVector_0.16.0 GenomeInfoDbData_0.99.0 RCurl_1.95-4.8 [7] bitops_1.0-6 _______________________________________________ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=bDabOgHqmutD8tE7VRQOn6ItcvsQOsLTpqQK4P7TwSo&s=WX_xk1if47kTfxxMZBFJwJtSReb1iLnoFpyPE9M-Diw&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