Replacing GRanges mcol makes it inaccessible

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Shraddha Pai ▴ 80

@shraddha-pai-5861

Last seen 9.6 years ago

Hi all, After I update the metadata on a Granges() object, I can no longer access the object. This happens on a Granges() object generated from the GFF3 file; I don't know if that matters. Here is the code to reproduce the error message. The gff file in question is from miRbase: ftp://mirbase.org/pub/mirbase/CURRENT/genomes/hsa.gff3 Has anyone else experienced this problem? Is there something different about a GRanges object generated by import()? I have also tried first setting mcols() to NULL and then doing mcols(x) <- tmp (putting in my new content), but that results in the same error. Thanks in advance, Shraddha ----- Shraddha Pai, Ph.D. Post-doctoral fellow Krembil Family Epigenetic Research Laboratory (Lab head: Dr. Art Petronis) Centre for Addiction and Mental Health, Toronto ------------------------------------------- > require(rtracklayer) > x <- import("hsa.gff3") > tmp <- mcols(x) > tmp <- cbind(as.data.frame(tmp), new_column="abc") > head(x) GRanges with 6 ranges and 8 metadata columns: seqnames ranges strand | source type <rle> <iranges> <rle> | <factor> <factor> [1] chr1 [ 17369, 17436] - | <na> miRNA_primary_transcript [2] chr1 [ 17409, 17431] - | <na> miRNA [3] chr1 [ 17369, 17391] - | <na> miRNA [4] chr1 [ 30366, 30503] + | <na> miRNA_primary_transcript [5] chr1 [ 30438, 30458] + | <na> miRNA [6] chr1 [567705, 567793] - | <na> miRNA_primary_transcript score phase ID Alias Name <numeric> <integer> <character> <characterlist> <character> [1] <na> <na> MI0022705 MI0022705 hsa-mir-6859-1 [2] <na> <na> MIMAT0027618 MIMAT0027618 hsa-miR-6859-5p [3] <na> <na> MIMAT0027619 MIMAT0027619 hsa-miR-6859-3p [4] <na> <na> MI0006363 MI0006363 hsa-mir-1302-2 [5] <na> <na> MIMAT0005890 MIMAT0005890 hsa-miR-1302 [6] <na> <na> MI0022558 MI0022558 hsa-mir-6723 Derives_from <character> [1] <na> [2] MI0022705 [3] MI0022705 [4] <na> [5] MI0006363 [6] <na> --- seqlengths: chr1 chr10 chr11 chr12 chr13 chr14 ... chr6 chr7 chr8 chr9 chrX chrY NA NA NA NA NA NA ... NA NA NA NA NA NA > mcols(x) <- tmp > head(x) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'extractROWS' for signature '"AsIs"' > x GRanges with 4665 ranges and 9 metadata columns: Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'extractROWS' for signature '"AsIs"' ---- Here is the output from sessionInfo() > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] rtracklayer_1.22.2 GenomicRanges_1.14.4 XVector_0.2.0 [4] IRanges_1.20.6 BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] BSgenome_1.30.0 Biostrings_2.30.1 RCurl_1.95-4.1 Rsamtools_1.14.2 [5] XML_3.98-1.1 bitops_1.0-6 stats4_3.0.1 tools_3.0.1 [9] zlibbioc_1.8.0

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ADD COMMENT • link updated 9.9 years ago by Michael Lawrence ★ 11k • written 9.9 years ago by Shraddha Pai ▴ 80

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Michael Lawrence ★ 11k

@michael-lawrence-3846

Last seen 2.4 years ago

United States

On Fri, May 30, 2014 at 8:48 AM, Shraddha Pai <shraddha.pai@camh.ca> wrote: > Hi all, > After I update the metadata on a Granges() object, I can no longer access > the object. This happens on a Granges() object generated from the GFF3 > file; I don't know if that matters. > > Here is the code to reproduce the error message. The gff file in question > is from miRbase: ftp://mirbase.org/pub/mirbase/CURRENT/genomes/hsa.gff3 > > Has anyone else experienced this problem? Is there something different > about a GRanges object generated by import()? > I have also tried first setting mcols() to NULL and then doing mcols(x) <- > tmp (putting in my new content), but that results in the same error. > > Thanks in advance, > Shraddha > ----- > Shraddha Pai, Ph.D. > Post-doctoral fellow > Krembil Family Epigenetic Research Laboratory (Lab head: Dr. Art Petronis) > Centre for Addiction and Mental Health, Toronto > > ------------------------------------------- > > > > require(rtracklayer) > > x <- import("hsa.gff3") > > tmp <- mcols(x) > > tmp <- cbind(as.data.frame(tmp), new_column="abc") > I think you want either: mcols(x)$new_column <- "abs" or the shortcut: x$new_column <- "abs" This a bug though; will fix. > head(x) > GRanges with 6 ranges and 8 metadata columns: > seqnames ranges strand | source type > <rle> <iranges> <rle> | <factor> <factor> > [1] chr1 [ 17369, 17436] - | <na> miRNA_primary_transcript > [2] chr1 [ 17409, 17431] - | <na> miRNA > [3] chr1 [ 17369, 17391] - | <na> miRNA > [4] chr1 [ 30366, 30503] + | <na> miRNA_primary_transcript > [5] chr1 [ 30438, 30458] + | <na> miRNA > [6] chr1 [567705, 567793] - | <na> miRNA_primary_transcript > score phase ID Alias Name > <numeric> <integer> <character> <characterlist> <character> > [1] <na> <na> MI0022705 MI0022705 hsa- mir-6859-1 > [2] <na> <na> MIMAT0027618 MIMAT0027618 hsa- miR-6859-5p > [3] <na> <na> MIMAT0027619 MIMAT0027619 hsa- miR-6859-3p > [4] <na> <na> MI0006363 MI0006363 hsa- mir-1302-2 > [5] <na> <na> MIMAT0005890 MIMAT0005890 hsa- miR-1302 > [6] <na> <na> MI0022558 MI0022558 hsa- mir-6723 > Derives_from > <character> > [1] <na> > [2] MI0022705 > [3] MI0022705 > [4] <na> > [5] MI0006363 > [6] <na> > --- > seqlengths: > chr1 chr10 chr11 chr12 chr13 chr14 ... chr6 chr7 chr8 chr9 chrX > chrY > NA NA NA NA NA NA ... NA NA NA NA NA > NA > > mcols(x) <- tmp > > head(x) > Error in (function (classes, fdef, mtable) : > unable to find an inherited method for function 'extractROWS' for > signature '"AsIs"' > > x > GRanges with 4665 ranges and 9 metadata columns: > Error in (function (classes, fdef, mtable) : > unable to find an inherited method for function 'extractROWS' for > signature '"AsIs"' > > ---- > Here is the output from sessionInfo() > > sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] rtracklayer_1.22.2 GenomicRanges_1.14.4 XVector_0.2.0 > [4] IRanges_1.20.6 BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] BSgenome_1.30.0 Biostrings_2.30.1 RCurl_1.95-4.1 Rsamtools_1.14.2 > [5] XML_3.98-1.1 bitops_1.0-6 stats4_3.0.1 tools_3.0.1 > [9] zlibbioc_1.8.0 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

ADD COMMENT • link 9.9 years ago Michael Lawrence ★ 11k

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Hi Michael, Yes, doing : mcols(x)$new_column <- "abc" got rid of the error. Thanks very much for the prompt response. Shraddha From: Michael Lawrence <lawrence.michael@gene.com<mailto:lawrence.michael@gene.com>> Date: Friday, 30 May, 2014 11:55 AM To: Shraddha Pai <shraddha.pai@camh.ca<mailto:shraddha.pai@camh.ca>> Cc: "bioconductor@r-project.org<mailto:bioconductor@r-project.org>" <bioconductor@r-project.org<mailto:bioconductor@r-project.org>> Subject: Re: [BioC] Replacing GRanges mcol makes it inaccessible On Fri, May 30, 2014 at 8:48 AM, Shraddha Pai <shraddha.pai@camh.ca<mailto:shraddha.pai@camh.ca>> wrote: Hi all, After I update the metadata on a Granges() object, I can no longer access the object. This happens on a Granges() object generated from the GFF3 file; I don't know if that matters. Here is the code to reproduce the error message. The gff file in question is from miRbase: ftp://mirbase.org/pub/mirbase/CURRENT/genomes/hsa.gff3 Has anyone else experienced this problem? Is there something different about a GRanges object generated by import()? I have also tried first setting mcols() to NULL and then doing mcols(x) <- tmp (putting in my new content), but that results in the same error. Thanks in advance, Shraddha ----- Shraddha Pai, Ph.D. Post-doctoral fellow Krembil Family Epigenetic Research Laboratory (Lab head: Dr. Art Petronis) Centre for Addiction and Mental Health, Toronto ------------------------------------------- > require(rtracklayer) > x <- import("hsa.gff3") > tmp <- mcols(x) > tmp <- cbind(as.data.frame(tmp), new_column="abc") I think you want either: mcols(x)$new_column <- "abs" or the shortcut: x$new_column <- "abs" This a bug though; will fix. > head(x) GRanges with 6 ranges and 8 metadata columns: seqnames ranges strand | source type <rle> <iranges> <rle> | <factor> <factor> [1] chr1 [ 17369, 17436] - | <na> miRNA_primary_transcript [2] chr1 [ 17409, 17431] - | <na> miRNA [3] chr1 [ 17369, 17391] - | <na> miRNA [4] chr1 [ 30366, 30503] + | <na> miRNA_primary_transcript [5] chr1 [ 30438, 30458] + | <na> miRNA [6] chr1 [567705, 567793] - | <na> miRNA_primary_transcript score phase ID Alias Name <numeric> <integer> <character> <characterlist> <character> [1] <na> <na> MI0022705 MI0022705 hsa-mir-6859-1 [2] <na> <na> MIMAT0027618 MIMAT0027618 hsa-miR-6859-5p [3] <na> <na> MIMAT0027619 MIMAT0027619 hsa-miR-6859-3p [4] <na> <na> MI0006363 MI0006363 hsa-mir-1302-2 [5] <na> <na> MIMAT0005890 MIMAT0005890 hsa-miR-1302 [6] <na> <na> MI0022558 MI0022558 hsa-mir-6723 Derives_from <character> [1] <na> [2] MI0022705 [3] MI0022705 [4] <na> [5] MI0006363 [6] <na> --- seqlengths: chr1 chr10 chr11 chr12 chr13 chr14 ... chr6 chr7 chr8 chr9 chrX chrY NA NA NA NA NA NA ... NA NA NA NA NA NA > mcols(x) <- tmp > head(x) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'extractROWS' for signature '"AsIs"' > x GRanges with 4665 ranges and 9 metadata columns: Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'extractROWS' for signature '"AsIs"' ---- Here is the output from sessionInfo() > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] rtracklayer_1.22.2 GenomicRanges_1.14.4 XVector_0.2.0 [4] IRanges_1.20.6 BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] BSgenome_1.30.0 Biostrings_2.30.1 RCurl_1.95-4.1 Rsamtools_1.14.2 [5] XML_3.98-1.1 bitops_1.0-6 stats4_3.0.1 tools_3.0.1 [9] zlibbioc_1.8.0 _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org<mailto:bioconductor@r-project.org> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ______________________________________________________________________ This email has been scanned by the CAMH Email Security System. ______________________________________________________________________ [[alternative HTML version deleted]]

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