transport mcols from one GRange obejct to another

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Entering edit mode

Wim Kreinen ▴ 100

@wim-kreinen-5642

Last seen 11.2 years ago

Hello, I have 2 GRange objects gr1 and gr2 (with the same names but in a different order!) and I would like to "transport" the mcols of gr1 to gr2 - of course suitable for the names. Please ignore IRanges data. The problem must be solved only via the names. gr1 GRanges with 5 ranges and 2 metadata columns: seqnames ranges strand | score data <rle> <iranges> <rle> | <factor> <numeric> rs3737728 chr1 [1021365, 1021375] * | 0.340955 4 rs9651273 chr1 [1030515, 1030525] * | 0.438123 5 rs6687776 chr1 [1031490, 1031500] * | 0.196662 6 rs4970405 chr1 [1048905, 1048915] * | 0.208463 7 rs12726255 chr1 [1049900, 1049910] * | 0.433541 8 --- seqlengths: chr1 chr10 ... chrX chrY NA NA ... NA NA > gr2 GRanges with 5 ranges and 0 metadata columns: seqnames ranges strand <rle> <iranges> <rle> rs3737728 chr1 [1021415, 1021415] * rs6687776 chr1 [1030565, 1030565] * rs9651273 chr1 [1031540, 1031540] * rs4970405 chr1 [1048955, 1048955] * rs12726255 chr1 [1049950, 1049950] * --- seqlengths: chr1 chr10 ... chrX chrY NA NA ... NA NA > Thanks Wim class (drei) [1] "data.frame" > dput (gr1) new("GRanges" , seqnames = new("Rle" , values = structure(1L, .Label = c("chr1", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr17_ctg5_hap1", "chr18", "chr19", "chr2", "chr20", "chr21", "chr22", "chr3", "chr4", "chr4_ctg9_hap1", "chr5", "chr6", "chr6_apd_hap1", "chr6_cox_hap2", "chr6_dbb_hap3", "chr6_mann_hap4", "chr6_mcf_hap5", "chr6_qbl_hap6", "chr6_ssto_hap7", "chr7", "chr8", "chr9", "chrM", "chrX", "chrY"), class = "factor") , lengths = 5L , elementMetadata = NULL , metadata = list() ) , ranges = new("IRanges" , start = c(1021365L, 1030515L, 1031490L, 1048905L, 1049900L) , width = c(11L, 11L, 11L, 11L, 11L) , NAMES = c("rs3737728", "rs9651273", "rs6687776", "rs4970405", "rs12726255" ) , elementType = "integer" , elementMetadata = NULL , metadata = list() ) , strand = new("Rle" , values = structure(3L, .Label = c("+", "-", "*"), class = "factor") , lengths = 5L , elementMetadata = NULL , metadata = list() ) , elementMetadata = new("DataFrame" , rownames = NULL , nrows = 5L , listData = structure(list(score = structure(c(3L, 5L, 1L, 2L, 4L), .Label = c("0.196662", "0.208463", "0.340955", "0.433541", "0.438123"), class = "factor"), data = c(4, 5, 6, 7, 8)), .Names = c("score", "data")) , elementType = "ANY" , elementMetadata = NULL , metadata = list() ) , seqinfo = new("Seqinfo" , seqnames = c("chr1", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr17_ctg5_hap1", "chr18", "chr19", "chr2", "chr20", "chr21", "chr22", "chr3", "chr4", "chr4_ctg9_hap1", "chr5", "chr6", "chr6_apd_hap1", "chr6_cox_hap2", "chr6_dbb_hap3", "chr6_mann_hap4", "chr6_mcf_hap5", "chr6_qbl_hap6", "chr6_ssto_hap7", "chr7", "chr8", "chr9", "chrM", "chrX", "chrY") , seqlengths = c(NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_) , is_circular = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA) , genome = c(NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_ ) ) , metadata = list() ) > dput (gr2) new("GRanges" , seqnames = new("Rle" , values = structure(1L, .Label = c("chr1", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr17_ctg5_hap1", "chr18", "chr19", "chr2", "chr20", "chr21", "chr22", "chr3", "chr4", "chr4_ctg9_hap1", "chr5", "chr6", "chr6_apd_hap1", "chr6_cox_hap2", "chr6_dbb_hap3", "chr6_mann_hap4", "chr6_mcf_hap5", "chr6_qbl_hap6", "chr6_ssto_hap7", "chr7", "chr8", "chr9", "chrM", "chrX", "chrY"), class = "factor") , lengths = 5L , elementMetadata = NULL , metadata = list() ) , ranges = new("IRanges" , start = c(1021415L, 1030565L, 1031540L, 1048955L, 1049950L) , width = c(1L, 1L, 1L, 1L, 1L) , NAMES = c("rs3737728", "rs6687776", "rs9651273", "rs4970405", "rs12726255" ) , elementType = "integer" , elementMetadata = NULL , metadata = list() ) , strand = new("Rle" , values = structure(3L, .Label = c("+", "-", "*"), class = "factor") , lengths = 5L , elementMetadata = NULL , metadata = list() ) , elementMetadata = new("DataFrame" , rownames = NULL , nrows = 5L , listData = structure(list(), .Names = character(0)) , elementType = "ANY" , elementMetadata = NULL , metadata = list() ) , seqinfo = new("Seqinfo" , seqnames = c("chr1", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr17_ctg5_hap1", "chr18", "chr19", "chr2", "chr20", "chr21", "chr22", "chr3", "chr4", "chr4_ctg9_hap1", "chr5", "chr6", "chr6_apd_hap1", "chr6_cox_hap2", "chr6_dbb_hap3", "chr6_mann_hap4", "chr6_mcf_hap5", "chr6_qbl_hap6", "chr6_ssto_hap7", "chr7", "chr8", "chr9", "chrM", "chrX", "chrY") , seqlengths = c(NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_) , is_circular = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA) , genome = c(NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, NA_character_ ) ) , metadata = list() ) > [[alternative HTML version deleted]]

IRanges IRanges • 1.3k views

ADD COMMENT • link updated 12.5 years ago by Martin Morgan 25k • written 12.5 years ago by Wim Kreinen ▴ 100

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Entering edit mode

Martin Morgan 25k

@martin-morgan-1513

Last seen 9 months ago

United States

On 04/26/2013 03:33 PM, Wim Kreinen wrote: > Hello, > > I have 2 GRange objects gr1 and gr2 (with the same names but in a different > order!) and I would like to "transport" the mcols of gr1 to gr2 - of course > suitable for the names. I think you're looking to use `mcols` to get the metadata columns (DataFrame) from gr1, to reorder the rows to match gr2, and to use the "setter" `mcols<-` on to assign the columns to gr2, idx = match(names(gr2), names(gr1)) mcols(gr2) <- mcols(gr1)[idx,] actually, if the GRanges really are the same, you could idx = match(gr2, gr1) mcols(gr2) <- mcols(gr1)[idx,] but doing that for your ranges gives > match(gr2, gr1) [1] NA NA NA NA NA because the ranges don't match, even though the names do! Hopefully that's something you're expecting... Martin > > Please ignore IRanges data. The problem must be solved only via the names. > > gr1 > GRanges with 5 ranges and 2 metadata columns: > seqnames ranges strand | score data > <rle> <iranges> <rle> | <factor> <numeric> > rs3737728 chr1 [1021365, 1021375] * | 0.340955 4 > rs9651273 chr1 [1030515, 1030525] * | 0.438123 5 > rs6687776 chr1 [1031490, 1031500] * | 0.196662 6 > rs4970405 chr1 [1048905, 1048915] * | 0.208463 7 > rs12726255 chr1 [1049900, 1049910] * | 0.433541 8 > --- > seqlengths: > chr1 chr10 ... chrX chrY > NA NA ... NA NA >> gr2 > GRanges with 5 ranges and 0 metadata columns: > seqnames ranges strand > <rle> <iranges> <rle> > rs3737728 chr1 [1021415, 1021415] * > rs6687776 chr1 [1030565, 1030565] * > rs9651273 chr1 [1031540, 1031540] * > rs4970405 chr1 [1048955, 1048955] * > rs12726255 chr1 [1049950, 1049950] * > --- > seqlengths: > chr1 chr10 ... chrX chrY > NA NA ... NA NA >> > > Thanks > Wim > > class (drei) > [1] "data.frame" >> dput (gr1) > new("GRanges" > , seqnames = new("Rle" > , values = structure(1L, .Label = c("chr1", "chr10", "chr11", "chr12", > "chr13", > "chr14", "chr15", "chr16", "chr17", "chr17_ctg5_hap1", "chr18", > "chr19", "chr2", "chr20", "chr21", "chr22", "chr3", "chr4", > "chr4_ctg9_hap1", > "chr5", "chr6", "chr6_apd_hap1", "chr6_cox_hap2", "chr6_dbb_hap3", > "chr6_mann_hap4", "chr6_mcf_hap5", "chr6_qbl_hap6", "chr6_ssto_hap7", > "chr7", "chr8", "chr9", "chrM", "chrX", "chrY"), class = "factor") > , lengths = 5L > , elementMetadata = NULL > , metadata = list() > ) > , ranges = new("IRanges" > , start = c(1021365L, 1030515L, 1031490L, 1048905L, 1049900L) > , width = c(11L, 11L, 11L, 11L, 11L) > , NAMES = c("rs3737728", "rs9651273", "rs6687776", "rs4970405", > "rs12726255" > ) > , elementType = "integer" > , elementMetadata = NULL > , metadata = list() > ) > , strand = new("Rle" > , values = structure(3L, .Label = c("+", "-", "*"), class = "factor") > , lengths = 5L > , elementMetadata = NULL > , metadata = list() > ) > , elementMetadata = new("DataFrame" > , rownames = NULL > , nrows = 5L > , listData = structure(list(score = structure(c(3L, 5L, 1L, 2L, 4L), > .Label = c("0.196662", > "0.208463", "0.340955", "0.433541", "0.438123"), class = "factor"), > data = c(4, 5, 6, 7, 8)), .Names = c("score", "data")) > , elementType = "ANY" > , elementMetadata = NULL > , metadata = list() > ) > , seqinfo = new("Seqinfo" > , seqnames = c("chr1", "chr10", "chr11", "chr12", "chr13", "chr14", > "chr15", > "chr16", "chr17", "chr17_ctg5_hap1", "chr18", "chr19", "chr2", > "chr20", "chr21", "chr22", "chr3", "chr4", "chr4_ctg9_hap1", > "chr5", "chr6", "chr6_apd_hap1", "chr6_cox_hap2", "chr6_dbb_hap3", > "chr6_mann_hap4", "chr6_mcf_hap5", "chr6_qbl_hap6", "chr6_ssto_hap7", > "chr7", "chr8", "chr9", "chrM", "chrX", "chrY") > , seqlengths = c(NA_integer_, NA_integer_, NA_integer_, NA_integer_, > NA_integer_, > NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, > NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, > NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, > NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, > NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, > NA_integer_, NA_integer_, NA_integer_, NA_integer_) > , is_circular = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, > NA, NA, > NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, > NA, NA, NA) > , genome = c(NA_character_, NA_character_, NA_character_, > NA_character_, > NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, > NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, > NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, > NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, > NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, > NA_character_, NA_character_, NA_character_, NA_character_, NA_character_ > ) > ) > , metadata = list() > ) >> dput (gr2) > new("GRanges" > , seqnames = new("Rle" > , values = structure(1L, .Label = c("chr1", "chr10", "chr11", "chr12", > "chr13", > "chr14", "chr15", "chr16", "chr17", "chr17_ctg5_hap1", "chr18", > "chr19", "chr2", "chr20", "chr21", "chr22", "chr3", "chr4", > "chr4_ctg9_hap1", > "chr5", "chr6", "chr6_apd_hap1", "chr6_cox_hap2", "chr6_dbb_hap3", > "chr6_mann_hap4", "chr6_mcf_hap5", "chr6_qbl_hap6", "chr6_ssto_hap7", > "chr7", "chr8", "chr9", "chrM", "chrX", "chrY"), class = "factor") > , lengths = 5L > , elementMetadata = NULL > , metadata = list() > ) > , ranges = new("IRanges" > , start = c(1021415L, 1030565L, 1031540L, 1048955L, 1049950L) > , width = c(1L, 1L, 1L, 1L, 1L) > , NAMES = c("rs3737728", "rs6687776", "rs9651273", "rs4970405", > "rs12726255" > ) > , elementType = "integer" > , elementMetadata = NULL > , metadata = list() > ) > , strand = new("Rle" > , values = structure(3L, .Label = c("+", "-", "*"), class = "factor") > , lengths = 5L > , elementMetadata = NULL > , metadata = list() > ) > , elementMetadata = new("DataFrame" > , rownames = NULL > , nrows = 5L > , listData = structure(list(), .Names = character(0)) > , elementType = "ANY" > , elementMetadata = NULL > , metadata = list() > ) > , seqinfo = new("Seqinfo" > , seqnames = c("chr1", "chr10", "chr11", "chr12", "chr13", "chr14", > "chr15", > "chr16", "chr17", "chr17_ctg5_hap1", "chr18", "chr19", "chr2", > "chr20", "chr21", "chr22", "chr3", "chr4", "chr4_ctg9_hap1", > "chr5", "chr6", "chr6_apd_hap1", "chr6_cox_hap2", "chr6_dbb_hap3", > "chr6_mann_hap4", "chr6_mcf_hap5", "chr6_qbl_hap6", "chr6_ssto_hap7", > "chr7", "chr8", "chr9", "chrM", "chrX", "chrY") > , seqlengths = c(NA_integer_, NA_integer_, NA_integer_, NA_integer_, > NA_integer_, > NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, > NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, > NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, > NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, > NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, > NA_integer_, NA_integer_, NA_integer_, NA_integer_) > , is_circular = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, > NA, NA, > NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, > NA, NA, NA) > , genome = c(NA_character_, NA_character_, NA_character_, > NA_character_, > NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, > NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, > NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, > NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, > NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, > NA_character_, NA_character_, NA_character_, NA_character_, NA_character_ > ) > ) > , metadata = list() > ) >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793

ADD COMMENT • link 12.5 years ago Martin Morgan 25k

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Entering edit mode

Thank you This works: idx = match(names(gr2), names(gr1)) mcols(gr2) <- mcols(gr1)[idx,] Thanks again Wim 2013/4/27 Martin Morgan <mtmorgan@fhcrc.org> > On 04/26/2013 03:33 PM, Wim Kreinen wrote: > >> Hello, >> >> I have 2 GRange objects gr1 and gr2 (with the same names but in a >> different >> order!) and I would like to "transport" the mcols of gr1 to gr2 - of >> course >> suitable for the names. >> > > I think you're looking to use `mcols` to get the metadata columns > (DataFrame) from gr1, to reorder the rows to match gr2, and to use the > "setter" `mcols<-` on to assign the columns to gr2, > > idx = match(names(gr2), names(gr1)) > mcols(gr2) <- mcols(gr1)[idx,] > > actually, if the GRanges really are the same, you could > > idx = match(gr2, gr1) > mcols(gr2) <- mcols(gr1)[idx,] > > but doing that for your ranges gives > > > match(gr2, gr1) > [1] NA NA NA NA NA > > because the ranges don't match, even though the names do! Hopefully that's > something you're expecting... > > Martin > > >> Please ignore IRanges data. The problem must be solved only via the names. >> >> gr1 >> GRanges with 5 ranges and 2 metadata columns: >> seqnames ranges strand | score data >> <rle> <iranges> <rle> | <factor> <numeric> >> rs3737728 chr1 [1021365, 1021375] * | 0.340955 4 >> rs9651273 chr1 [1030515, 1030525] * | 0.438123 5 >> rs6687776 chr1 [1031490, 1031500] * | 0.196662 6 >> rs4970405 chr1 [1048905, 1048915] * | 0.208463 7 >> rs12726255 chr1 [1049900, 1049910] * | 0.433541 8 >> --- >> seqlengths: >> chr1 chr10 ... chrX chrY >> NA NA ... NA NA >> >>> gr2 >>> >> GRanges with 5 ranges and 0 metadata columns: >> seqnames ranges strand >> <rle> <iranges> <rle> >> rs3737728 chr1 [1021415, 1021415] * >> rs6687776 chr1 [1030565, 1030565] * >> rs9651273 chr1 [1031540, 1031540] * >> rs4970405 chr1 [1048955, 1048955] * >> rs12726255 chr1 [1049950, 1049950] * >> --- >> seqlengths: >> chr1 chr10 ... chrX chrY >> NA NA ... NA NA >> >>> >>> >> Thanks >> Wim >> >> class (drei) >> [1] "data.frame" >> >>> dput (gr1) >>> >> new("GRanges" >> , seqnames = new("Rle" >> , values = structure(1L, .Label = c("chr1", "chr10", "chr11", >> "chr12", >> "chr13", >> "chr14", "chr15", "chr16", "chr17", "chr17_ctg5_hap1", "chr18", >> "chr19", "chr2", "chr20", "chr21", "chr22", "chr3", "chr4", >> "chr4_ctg9_hap1", >> "chr5", "chr6", "chr6_apd_hap1", "chr6_cox_hap2", "chr6_dbb_hap3", >> "chr6_mann_hap4", "chr6_mcf_hap5", "chr6_qbl_hap6", "chr6_ssto_hap7", >> "chr7", "chr8", "chr9", "chrM", "chrX", "chrY"), class = "factor") >> , lengths = 5L >> , elementMetadata = NULL >> , metadata = list() >> ) >> , ranges = new("IRanges" >> , start = c(1021365L, 1030515L, 1031490L, 1048905L, 1049900L) >> , width = c(11L, 11L, 11L, 11L, 11L) >> , NAMES = c("rs3737728", "rs9651273", "rs6687776", "rs4970405", >> "rs12726255" >> ) >> , elementType = "integer" >> , elementMetadata = NULL >> , metadata = list() >> ) >> , strand = new("Rle" >> , values = structure(3L, .Label = c("+", "-", "*"), class = "factor") >> , lengths = 5L >> , elementMetadata = NULL >> , metadata = list() >> ) >> , elementMetadata = new("DataFrame" >> , rownames = NULL >> , nrows = 5L >> , listData = structure(list(score = structure(c(3L, 5L, 1L, 2L, 4L), >> .Label = c("0.196662", >> "0.208463", "0.340955", "0.433541", "0.438123"), class = "factor"), >> data = c(4, 5, 6, 7, 8)), .Names = c("score", "data")) >> , elementType = "ANY" >> , elementMetadata = NULL >> , metadata = list() >> ) >> , seqinfo = new("Seqinfo" >> , seqnames = c("chr1", "chr10", "chr11", "chr12", "chr13", "chr14", >> "chr15", >> "chr16", "chr17", "chr17_ctg5_hap1", "chr18", "chr19", "chr2", >> "chr20", "chr21", "chr22", "chr3", "chr4", "chr4_ctg9_hap1", >> "chr5", "chr6", "chr6_apd_hap1", "chr6_cox_hap2", "chr6_dbb_hap3", >> "chr6_mann_hap4", "chr6_mcf_hap5", "chr6_qbl_hap6", "chr6_ssto_hap7", >> "chr7", "chr8", "chr9", "chrM", "chrX", "chrY") >> , seqlengths = c(NA_integer_, NA_integer_, NA_integer_, NA_integer_, >> NA_integer_, >> NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, >> NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, >> NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, >> NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, >> NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, >> NA_integer_, NA_integer_, NA_integer_, NA_integer_) >> , is_circular = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, >> NA, NA, >> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, >> NA, NA, NA) >> , genome = c(NA_character_, NA_character_, NA_character_, >> NA_character_, >> NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, >> NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, >> NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, >> NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, >> NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, >> NA_character_, NA_character_, NA_character_, NA_character_, NA_character_ >> ) >> ) >> , metadata = list() >> ) >> >>> dput (gr2) >>> >> new("GRanges" >> , seqnames = new("Rle" >> , values = structure(1L, .Label = c("chr1", "chr10", "chr11", >> "chr12", >> "chr13", >> "chr14", "chr15", "chr16", "chr17", "chr17_ctg5_hap1", "chr18", >> "chr19", "chr2", "chr20", "chr21", "chr22", "chr3", "chr4", >> "chr4_ctg9_hap1", >> "chr5", "chr6", "chr6_apd_hap1", "chr6_cox_hap2", "chr6_dbb_hap3", >> "chr6_mann_hap4", "chr6_mcf_hap5", "chr6_qbl_hap6", "chr6_ssto_hap7", >> "chr7", "chr8", "chr9", "chrM", "chrX", "chrY"), class = "factor") >> , lengths = 5L >> , elementMetadata = NULL >> , metadata = list() >> ) >> , ranges = new("IRanges" >> , start = c(1021415L, 1030565L, 1031540L, 1048955L, 1049950L) >> , width = c(1L, 1L, 1L, 1L, 1L) >> , NAMES = c("rs3737728", "rs6687776", "rs9651273", "rs4970405", >> "rs12726255" >> ) >> , elementType = "integer" >> , elementMetadata = NULL >> , metadata = list() >> ) >> , strand = new("Rle" >> , values = structure(3L, .Label = c("+", "-", "*"), class = "factor") >> , lengths = 5L >> , elementMetadata = NULL >> , metadata = list() >> ) >> , elementMetadata = new("DataFrame" >> , rownames = NULL >> , nrows = 5L >> , listData = structure(list(), .Names = character(0)) >> , elementType = "ANY" >> , elementMetadata = NULL >> , metadata = list() >> ) >> , seqinfo = new("Seqinfo" >> , seqnames = c("chr1", "chr10", "chr11", "chr12", "chr13", "chr14", >> "chr15", >> "chr16", "chr17", "chr17_ctg5_hap1", "chr18", "chr19", "chr2", >> "chr20", "chr21", "chr22", "chr3", "chr4", "chr4_ctg9_hap1", >> "chr5", "chr6", "chr6_apd_hap1", "chr6_cox_hap2", "chr6_dbb_hap3", >> "chr6_mann_hap4", "chr6_mcf_hap5", "chr6_qbl_hap6", "chr6_ssto_hap7", >> "chr7", "chr8", "chr9", "chrM", "chrX", "chrY") >> , seqlengths = c(NA_integer_, NA_integer_, NA_integer_, NA_integer_, >> NA_integer_, >> NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, >> NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, >> NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, >> NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, >> NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, >> NA_integer_, NA_integer_, NA_integer_, NA_integer_) >> , is_circular = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, >> NA, NA, >> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, >> NA, NA, NA) >> , genome = c(NA_character_, NA_character_, NA_character_, >> NA_character_, >> NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, >> NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, >> NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, >> NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, >> NA_character_, NA_character_, NA_character_, NA_character_, NA_character_, >> NA_character_, NA_character_, NA_character_, NA_character_, NA_character_ >> ) >> ) >> , metadata = list() >> ) >> >>> >>> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> >> > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > [[alternative HTML version deleted]]

ADD REPLY • link 12.5 years ago Wim Kreinen ▴ 100

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