Hello, I recognised a strange behaviour of range (gr). Shouldnt it treat the whole grange object? Like ranges(gr)? But it doesnt. What's wrong? Thanks Hermann > gr GRanges with 4 ranges and 1 metadata column: seqnames ranges strand | score <rle> <iranges> <rle> | <character> rs55998931 chr1 [10492, 10492] * | 0.115787 rs58108140 chr1 [10583, 10583] * | 0.394721 rs75454623 chr1 [14930, 14930] * | 0.48 rs12401368 chr1 [66507, 66507] * | 0.499191 --- seqlengths: chr1 chr10 ... chrX chrY NA NA ... NA NA > ranges (gr) IRanges of length 4 start end width names [1] 10492 10492 1 rs55998931 [2] 10583 10583 1 rs58108140 [3] 14930 14930 1 rs75454623 [4] 66507 66507 1 rs12401368 > range (gr) # Only gives back gr[1] GRanges with 1 range and 0 metadata columns: seqnames ranges strand <rle> <iranges> <rle> [1] chr1 [10492, 66507] * --- seqlengths: chr1 chr10 ... chrX chrY NA NA ... NA NA > dput (gr) 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 = 4L , elementMetadata = NULL , metadata = list() ) , ranges = new("IRanges" , start = c(10492L, 10583L, 14930L, 66507L) , width = c(1L, 1L, 1L, 1L) , NAMES = c("rs55998931", "rs58108140", "rs75454623", "rs12401368") , elementType = "integer" , elementMetadata = NULL , metadata = list() ) , strand = new("Rle" , values = structure(3L, .Label = c("+", "-", "*"), class = "factor") , lengths = 4L , elementMetadata = NULL , metadata = list() ) , elementMetadata = new("DataFrame" , rownames = NULL , nrows = 4L , listData = structure(list(score = c("0.115787", "0.394721", "0.48", "0.499191" )), .Names = "score") , 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("hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19") ) , metadata = list(<s4 object="" of="" class="" structure("dataframe",="" package="IRanges" )="">) ) > SessionInfo() Fehler: konnte Funktion "SessionInfo" nicht finden > sessionInfo() R version 2.15.3 (2013-03-01) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GenABEL_1.7-4 MASS_7.3-23 GenomicRanges_1.10.7 [4] IRanges_1.16.6 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] compiler_2.15.3 parallel_2.15.3 stats4_2.15.3 tools_2.15.3 [[alternative HTML version deleted]]

Hi Hermann, You are mixing ranges() and range(). range() returns a range that spans the min/max of all arguments. ranges() on a GRanges will give you the IRanges. ?'range,GenomicRanges-method' ?'ranges,GRanges-method' Valerie On 04/09/2013 06:37 AM, Hermann Norpois wrote: > Hello, > > I recognised a strange behaviour of range (gr). Shouldnt it treat the whole > grange object? Like ranges(gr)? But it doesnt. > > What's wrong? > Thanks > Hermann > >> gr > GRanges with 4 ranges and 1 metadata column: > seqnames ranges strand | score > <rle> <iranges> <rle> | <character> > rs55998931 chr1 [10492, 10492] * | 0.115787 > rs58108140 chr1 [10583, 10583] * | 0.394721 > rs75454623 chr1 [14930, 14930] * | 0.48 > rs12401368 chr1 [66507, 66507] * | 0.499191 > --- > seqlengths: > chr1 chr10 ... chrX chrY > NA NA ... NA NA >> ranges (gr) > IRanges of length 4 > start end width names > [1] 10492 10492 1 rs55998931 > [2] 10583 10583 1 rs58108140 > [3] 14930 14930 1 rs75454623 > [4] 66507 66507 1 rs12401368 >> range (gr) # Only gives back gr[1] > GRanges with 1 range and 0 metadata columns: > seqnames ranges strand > <rle> <iranges> <rle> > [1] chr1 [10492, 66507] * > --- > seqlengths: > chr1 chr10 ... chrX chrY > NA NA ... NA NA >> dput (gr) > 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 = 4L > , elementMetadata = NULL > , metadata = list() > ) > , ranges = new("IRanges" > , start = c(10492L, 10583L, 14930L, 66507L) > , width = c(1L, 1L, 1L, 1L) > , NAMES = c("rs55998931", "rs58108140", "rs75454623", "rs12401368") > , elementType = "integer" > , elementMetadata = NULL > , metadata = list() > ) > , strand = new("Rle" > , values = structure(3L, .Label = c("+", "-", "*"), class = "factor") > , lengths = 4L > , elementMetadata = NULL > , metadata = list() > ) > , elementMetadata = new("DataFrame" > , rownames = NULL > , nrows = 4L > , listData = structure(list(score = c("0.115787", "0.394721", "0.48", > "0.499191" > )), .Names = "score") > , 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("hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", > "hg19", > "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", > "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", > "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", > "hg19", "hg19") > ) > , metadata = list(<s4 object="" of="" class="" structure("dataframe",="" package=""> "IRanges")>) > ) >> SessionInfo() > Fehler: konnte Funktion "SessionInfo" nicht finden >> sessionInfo() > R version 2.15.3 (2013-03-01) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C > [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 > [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] GenABEL_1.7-4 MASS_7.3-23 GenomicRanges_1.10.7 > [4] IRanges_1.16.6 BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] compiler_2.15.3 parallel_2.15.3 stats4_2.15.3 tools_2.15.3 > > [[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 >

Hi Hermann, On 04/09/2013 06:37 AM, Hermann Norpois wrote: > Hello, > > I recognised a strange behaviour of range (gr). Shouldnt it treat the whole > grange object? Like ranges(gr)? But it doesnt. > > What's wrong? > Thanks > Hermann > >> gr > GRanges with 4 ranges and 1 metadata column: > seqnames ranges strand | score > <rle> <iranges> <rle> | <character> > rs55998931 chr1 [10492, 10492] * | 0.115787 > rs58108140 chr1 [10583, 10583] * | 0.394721 > rs75454623 chr1 [14930, 14930] * | 0.48 > rs12401368 chr1 [66507, 66507] * | 0.499191 > --- > seqlengths: > chr1 chr10 ... chrX chrY > NA NA ... NA NA >> ranges (gr) > IRanges of length 4 > start end width names > [1] 10492 10492 1 rs55998931 > [2] 10583 10583 1 rs58108140 > [3] 14930 14930 1 rs75454623 > [4] 66507 66507 1 rs12401368 >> range (gr) # Only gives back gr[1] > GRanges with 1 range and 0 metadata columns: > seqnames ranges strand > <rle> <iranges> <rle> > [1] chr1 [10492, 66507] * > --- > seqlengths: > chr1 chr10 ... chrX chrY > NA NA ... NA NA This is the expected behavior: 1 range per distinct seqname / strand combination. So in your case, only 1 range, because everything is on chr1 / *. The fact that it happens to be the same as the 1st input range is because that range contains all the other ranges. But it's not always the case: > gr GRanges with 4 ranges and 0 metadata columns: seqnames ranges strand <rle> <iranges> <rle> [1] chr1 [ 7, 11] * [2] chr1 [ 6, 10] * [3] chr1 [ 5, 9] * [4] chr1 [20, 24] * --- seqlengths: chr1 NA > range(gr) GRanges with 1 range and 0 metadata columns: seqnames ranges strand <rle> <iranges> <rle> [1] chr1 [5, 24] * --- seqlengths: chr1 NA See ?`range,GenomicRanges-method` for the details and more examples. Cheers, H. >> dput (gr) > 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 = 4L > , elementMetadata = NULL > , metadata = list() > ) > , ranges = new("IRanges" > , start = c(10492L, 10583L, 14930L, 66507L) > , width = c(1L, 1L, 1L, 1L) > , NAMES = c("rs55998931", "rs58108140", "rs75454623", "rs12401368") > , elementType = "integer" > , elementMetadata = NULL > , metadata = list() > ) > , strand = new("Rle" > , values = structure(3L, .Label = c("+", "-", "*"), class = "factor") > , lengths = 4L > , elementMetadata = NULL > , metadata = list() > ) > , elementMetadata = new("DataFrame" > , rownames = NULL > , nrows = 4L > , listData = structure(list(score = c("0.115787", "0.394721", "0.48", > "0.499191" > )), .Names = "score") > , 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("hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", > "hg19", > "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", > "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", > "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", > "hg19", "hg19") > ) > , metadata = list(<s4 object="" of="" class="" structure("dataframe",="" package=""> "IRanges")>) > ) >> SessionInfo() > Fehler: konnte Funktion "SessionInfo" nicht finden >> sessionInfo() > R version 2.15.3 (2013-03-01) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C > [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 > [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] GenABEL_1.7-4 MASS_7.3-23 GenomicRanges_1.10.7 > [4] IRanges_1.16.6 BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] compiler_2.15.3 parallel_2.15.3 stats4_2.15.3 tools_2.15.3 > > [[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 > -- 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: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319