I have data as GRange object test.gr GRanges with 20 ranges and 0 metadata columns: seqnames ranges strand <rle> <iranges> <rle> [1] chr1 [ 10246, 10283] * [2] chr1 [237718, 237887] * [3] chr1 [521553, 521613] * [4] chr1 [564413, 564686] * or as classical dataframe head (test) seqnames start end width strand 1 chr1 10246 10283 38 * 2 chr1 237718 237887 170 * 3 chr1 521553 521613 61 * 4 chr1 564413 564686 274 * and I wish to count how often do intervals of a certain intervall exist. I would be happy to get something like this: width occurence of the width sum of the occurence 0-50 2 2 50-100 4 6 100-150 5 11 I would prefer to do this using the GRange object directly but I would be happy to know a way how to do it via test (classical dataframe). Could you please give me a hint. Thanks Hermann P.S.: My data > dput (test) structure(list(seqnames = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = c("chr1", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr2", "chr20", "chr21", "chr22", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chrX", "chrY"), class = "factor"), start = c(10246L, 237718L, 521553L, 564413L, 565252L, 566538L, 567450L, 568777L, 569457L, 669190L, 713884L, 740270L, 752164L, 753266L, 754421L, 762051L, 785811L, 786878L, 791087L, 793485L), end = c(10283L, 237887L, 521613L, 564686L, 566081L, 567275L, 568583L, 569302L, 570125L, 669259L, 714603L, 740423L, 752782L, 753697L, 754711L, 763151L, 786025L, 787053L, 791138L, 793582L), width = c(38L, 170L, 61L, 274L, 830L, 738L, 1134L, 526L, 669L, 70L, 720L, 154L, 619L, 432L, 291L, 1101L, 215L, 176L, 52L, 98L), strand = structure(c(3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), .Label = c("+", "-", "*"), class = "factor")), .Names = c("seqnames", "start", "end", "width", "strand"), row.names = c(NA, 20L), class = "data.frame") > dput test.gr) new("GRanges" , seqnames = new("Rle" , values = structure(1L, .Label = c("chr1", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr2", "chr20", "chr21", "chr22", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chrX", "chrY"), class = "factor") , lengths = 20L , elementMetadata = NULL , metadata = list() ) , ranges = new("IRanges" , start = c(10246L, 237718L, 521553L, 564413L, 565252L, 566538L, 567450L, 568777L, 569457L, 669190L, 713884L, 740270L, 752164L, 753266L, 754421L, 762051L, 785811L, 786878L, 791087L, 793485L) , width = c(38L, 170L, 61L, 274L, 830L, 738L, 1134L, 526L, 669L, 70L, 720L, 154L, 619L, 432L, 291L, 1101L, 215L, 176L, 52L, 98L) , NAMES = NULL , elementType = "integer" , elementMetadata = NULL , metadata = list() ) , strand = new("Rle" , values = structure(3L, .Label = c("+", "-", "*"), class = "factor") , lengths = 20L , elementMetadata = NULL , metadata = list() ) , elementMetadata = new("DataFrame" , rownames = NULL , nrows = 20L , 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", "chr18", "chr19", "chr2", "chr20", "chr21", "chr22", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "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_) , 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) , 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_ ) ) , metadata = list() ) > [[alternative HTML version deleted]]

Not at a computer so can't give a full answer, also it is not clear to me what your last column is ("sum of occurrence?"), but one way to count the number of intervals of predefined ranges of widths would be with the `cut` function. You could then tally the results from `cut` using the `table` or `tabulate` Reading through the relevant help pages along with their examples should make things a bit more clear. HTH, -steve On Sunday, December 23, 2012, Hermann Norpois wrote: > I have data as GRange object > > test.gr > GRanges with 20 ranges and 0 metadata columns: > seqnames ranges strand > <rle> <iranges> <rle> > [1] chr1 [ 10246, 10283] * > [2] chr1 [237718, 237887] * > [3] chr1 [521553, 521613] * > [4] chr1 [564413, 564686] * > > or as classical dataframe > > head (test) > seqnames start end width strand > 1 chr1 10246 10283 38 * > 2 chr1 237718 237887 170 * > 3 chr1 521553 521613 61 * > 4 chr1 564413 564686 274 * > > and I wish to count how often do intervals of a certain intervall exist. I > would be happy to get something like this: > > width occurence of the width sum of the occurence > 0-50 2 2 > 50-100 4 6 > 100-150 5 11 > > I would prefer to do this using the GRange object directly but I would be > happy to know a way how to do it via test (classical dataframe). > Could you please give me a hint. > > Thanks Hermann > > > P.S.: My data > > > dput (test) > structure(list(seqnames = structure(c(1L, 1L, 1L, 1L, 1L, 1L, > 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = c("chr1", > "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", > "chr17", "chr18", "chr19", "chr2", "chr20", "chr21", "chr22", > "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chrX", > "chrY"), class = "factor"), start = c(10246L, 237718L, 521553L, > 564413L, 565252L, 566538L, 567450L, 568777L, 569457L, 669190L, > 713884L, 740270L, 752164L, 753266L, 754421L, 762051L, 785811L, > 786878L, 791087L, 793485L), end = c(10283L, 237887L, 521613L, > 564686L, 566081L, 567275L, 568583L, 569302L, 570125L, 669259L, > 714603L, 740423L, 752782L, 753697L, 754711L, 763151L, 786025L, > 787053L, 791138L, 793582L), width = c(38L, 170L, 61L, 274L, 830L, > 738L, 1134L, 526L, 669L, 70L, 720L, 154L, 619L, 432L, 291L, 1101L, > 215L, 176L, 52L, 98L), strand = structure(c(3L, 3L, 3L, 3L, 3L, > 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), .Label = > c("+", > "-", "*"), class = "factor")), .Names = c("seqnames", "start", > "end", "width", "strand"), row.names = c(NA, 20L), class = "data.frame") > > dput test.gr) > new("GRanges" > , seqnames = new("Rle" > , values = structure(1L, .Label = c("chr1", "chr10", "chr11", "chr12", > "chr13", > "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr2", > "chr20", "chr21", "chr22", "chr3", "chr4", "chr5", "chr6", "chr7", > "chr8", "chr9", "chrX", "chrY"), class = "factor") > , lengths = 20L > , elementMetadata = NULL > , metadata = list() > ) > , ranges = new("IRanges" > , start = c(10246L, 237718L, 521553L, 564413L, 565252L, 566538L, > 567450L, > 568777L, 569457L, 669190L, 713884L, 740270L, 752164L, 753266L, > 754421L, 762051L, 785811L, 786878L, 791087L, 793485L) > , width = c(38L, 170L, 61L, 274L, 830L, 738L, 1134L, 526L, 669L, 70L, > 720L, > 154L, 619L, 432L, 291L, 1101L, 215L, 176L, 52L, 98L) > , NAMES = NULL > , elementType = "integer" > , elementMetadata = NULL > , metadata = list() > ) > , strand = new("Rle" > , values = structure(3L, .Label = c("+", "-", "*"), class = "factor") > , lengths = 20L > , elementMetadata = NULL > , metadata = list() > ) > , elementMetadata = new("DataFrame" > , rownames = NULL > , nrows = 20L > , 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", "chr18", "chr19", "chr2", "chr20", "chr21", > "chr22", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", > "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_) > , 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) > , 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_ > ) > ) > , metadata = list() > ) > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org <javascript:;> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact [[alternative HTML version deleted]]