Re: [Bioc-devel] strand<- method for 'GPos' doesn't work
hi Hervé, i had not imagine this could require so much code refactoring, so thanks a lot for the quick and extensive fix. i'll have a close look and let you know if i encounter any problem. thanks again!!! robert. On 07/20/2017 11:23 AM, Hervé Pagès wrote: Hi Robert, This should work in GenomicRanges 1.29.10. Note that working on this revealed some minor shortcomings of the GPos internal representation so I decided to change it. The new one relies on IPos, a new class in IRanges 2.11.10. IPos is analog to GPos but for "integer positions" instead of "genomic positions". See ?IPos for the details. The new GPos objects behave exactly like the old ones except for 2 things: - the strand() setter now works - ranges() now returns an IPos instead of an IRanges object Update any old GPos object 'x' with x <- updateObject(x, verbose=TRUE) Let me know if you run into any issue with this. Cheers, H. On 07/18/2017 03:00 PM, Robert Castelo wrote: great, thanks Hervé! robert. On 18/07/2017 20:57, Hervé Pagès wrote: 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: seqnamesranges strand [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: seqnamesranges strand [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.UTF8LC_COLLATE=en_US.UTF8 [5] LC_MONETARY=en_US.UTF8LC_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 stats4stats 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=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=bDabOgHqmutD8tE7VRQOn6ItcvsQOsLTpqQK4P7TwSo=WX_xk1if47kTfxxMZBFJwJtSReb1iLnoFpyPE9M-Diw= -- Robert Castelo, PhD Associate Professor Dept. of Experimental and Health Sciences Universitat Pompeu Fabra (UPF) Barcelona Biomedical Research Park (PRBB) Dr Aiguader 88 E-08003 Barcelona, Spain telf: +34.933.160.514 fax: +34.933.160.550 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] strand<- method for 'GPos' doesn't work
Hi Robert, This should work in GenomicRanges 1.29.10. Note that working on this revealed some minor shortcomings of the GPos internal representation so I decided to change it. The new one relies on IPos, a new class in IRanges 2.11.10. IPos is analog to GPos but for "integer positions" instead of "genomic positions". See ?IPos for the details. The new GPos objects behave exactly like the old ones except for 2 things: - the strand() setter now works - ranges() now returns an IPos instead of an IRanges object Update any old GPos object 'x' with x <- updateObject(x, verbose=TRUE) Let me know if you run into any issue with this. Cheers, H. On 07/18/2017 03:00 PM, Robert Castelo wrote: great, thanks Hervé! robert. On 18/07/2017 20:57, Hervé Pagès wrote: 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: seqnamesranges strand [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: seqnamesranges strand [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.UTF8LC_COLLATE=en_US.UTF8 [5] LC_MONETARY=en_US.UTF8LC_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 stats4stats 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=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=bDabOgHqmutD8tE7VRQOn6ItcvsQOsLTpqQK4P7TwSo=WX_xk1if47kTfxxMZBFJwJtSReb1iLnoFpyPE9M-Diw= -- 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
Re: [Bioc-devel] strand<- method for 'GPos' doesn't work
great, thanks Hervé! robert. On 18/07/2017 20:57, Hervé Pagès wrote: 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: seqnamesranges strand [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: seqnamesranges strand [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.UTF8LC_COLLATE=en_US.UTF8 [5] LC_MONETARY=en_US.UTF8LC_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 stats4stats 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=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=bDabOgHqmutD8tE7VRQOn6ItcvsQOsLTpqQK4P7TwSo=WX_xk1if47kTfxxMZBFJwJtSReb1iLnoFpyPE9M-Diw= ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] strand<- method for 'GPos' doesn't work
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: seqnamesranges strand [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: seqnamesranges strand [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.UTF8LC_COLLATE=en_US.UTF8 [5] LC_MONETARY=en_US.UTF8LC_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 stats4stats 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=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=bDabOgHqmutD8tE7VRQOn6ItcvsQOsLTpqQK4P7TwSo=WX_xk1if47kTfxxMZBFJwJtSReb1iLnoFpyPE9M-Diw= -- 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
[Bioc-devel] strand<- method for 'GPos' doesn't work
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: seqnamesranges strand [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: seqnamesranges strand [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.UTF8LC_COLLATE=en_US.UTF8 [5] LC_MONETARY=en_US.UTF8LC_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 stats4stats 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://stat.ethz.ch/mailman/listinfo/bioc-devel
