Herman, You must be using the release version of HiTC. Providing the output of sessionInfo() is also helpful when posting a question so others can see what versions you are using. I've put mine done so at the bottom of this post. The Genome_intervals class is present in the release version (1.2.0) but not in devel (1.3.2). The author must have decided to use GRanges objects instead (I've cc'd them on this email). In the mean time, here is an example of how to convert a 'Genome_intervals' to a 'GRanges'. Using the release version, there is an example of how to create object 'i' at the bottom of this man page, ?'Genome_intervals-class' > i Object of class Genome_intervals 2 base intervals and 2 inter-base intervals(*): chr01 [1, 2) chr01 [3, 5) chr02 [4, 6] * chr02 [8, 9) * annotation: seq_name inter_base 1 chr01 FALSE 2 chr01 FALSE 3 chr02 TRUE 4 chr02 TRUE You can create a GRanges from 'i' with the following code, > GRanges(annotation(i)$seq_name, IRanges(i at .Data[,1], i at .Data[,2])) GRanges with 4 ranges and 0 elementMetadata cols: seqnames ranges strand <rle> <iranges> <rle> [1] chr01 [1, 2] * [2] chr01 [3, 5] * [3] chr02 [4, 6] * [4] chr02 [8, 9] * --- seqlengths: chr01 chr02 NA NA > gr <- GRanges(annotation(i)$seq_name, IRanges(i at .Data[,1], i at .Data[,2])) You can add metadata with values() or elementMetadata(). These two functions have been replaced with mcols() in the devel branch. > values(gr) <- DataFrame("inter_base"=annotation(i)$inter_base) > gr GRanges with 4 ranges and 1 elementMetadata col: seqnames ranges strand | inter_base <rle> <iranges> <rle> | <logical> [1] chr01 [1, 2] * | FALSE [2] chr01 [3, 5] * | FALSE [3] chr02 [4, 6] * | TRUE [4] chr02 [8, 9] * | TRUE --- seqlengths: chr01 chr02 NA NA Valerie > sessionInfo() ... other attached packages: [1] HiTC_1.2.0 girafe_1.8.0 genomeIntervals_1.12.0 [4] intervals_0.13.3 ShortRead_1.14.4 latticeExtra_0.6-24 [7] RColorBrewer_1.0-5 lattice_0.20-10 Rsamtools_1.8.6 [10] Biostrings_2.24.1 GenomicRanges_1.8.13 IRanges_1.14.4 [13] BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] BSgenome_1.24.0 Biobase_2.16.0 bitops_1.0-5 hwriter_1.3 [5] stats4_2.15.1 tools_2.15.1 zlibbioc_1.2.0 On 02/06/13 09:13, Valerie Obenchain wrote: > Hi Herman, > > When you post a question please provide code that reproduces the > problem. Your example does not show how 'hic.gr' was created or what > kind of object it is. > > library(HiTC) > data(Nora_5C) > intervals <- y_intervals(E14sub) > > The 'intervals' object is a GRanges. > > > class(intervals) > [1] "GRanges" > attr(,"package") > [1] "GenomicRanges" > > You can extract metadata colums with 'mcols'. > > head(mcols(intervals)) > > > head(mcols(intervals)) > DataFrame with 6 rows and 4 columns > name score itemRgb thick > <character> <numeric> <character> <iranges> > 1 FOR_3 0 #0000FF [98834146, 98837506] > 2 FOR_5 0 #0000FF [98840772, 98841227] > 3 FOR_7 0 #0000FF [98843249, 98848364] > 4 FOR_9 0 #0000FF [98849664, 98850577] > 5 FOR_13 0 #0000FF [98862022, 98867230] > 6 FOR_15 0 #0000FF [98869143, 98870524] > > Also use 'mcols' to set the value of a metadata column. > > intervals$newData <- seq_along(intervals) > > head(mcols(intervals)) > DataFrame with 6 rows and 5 columns > name score itemRgb thick newData > <character> <numeric> <character> <iranges> <integer> > 1 FOR_3 0 #0000FF [98834146, 98837506] 1 > 2 FOR_5 0 #0000FF [98840772, 98841227] 2 > 3 FOR_7 0 #0000FF [98843249, 98848364] 3 > 4 FOR_9 0 #0000FF [98849664, 98850577] 4 > 5 FOR_13 0 #0000FF [98862022, 98867230] 5 > 6 FOR_15 0 #0000FF [98869143, 98870524] 6 > > > It looks like y_intervals() is returning a valid GRanges. Can you > provide an example of how you are getting a 'Genome_interval' object? > > Valerie > > > > On 02/05/2013 01:05 PM, Hermann Norpois wrote: >> Hello, >> >> in the documentation of HiTC package y_intervals () is described as a >> method to "return the ygi GRanges object defining the y intervals". I >> tried >> this for the test data (see dput) and expected a "classical" GRange >> object. >> For instance I would like to do an operation like >> >> mcols hic.gr)$test<- 1 >> >> But it did not work as hic.gr is a Genome_interval object (as dput >> mentioned). Can I transform this in a classical GR-object allowing >> mcols-operations? Can anybody comment on the difference between >> Genome_interval an Grange? >> >> >> Thanks >> Hermann >> >> >> >>> hic.gr >> Object of class Genome_intervals >> 5 base intervals and 0 inter-base intervals(*): >> chr14 [1, 999999] >> chr14 [1e+06, 1999999] >> chr14 [2e+06, 2999999] >> chr14 [3e+06, 3999999] >> chr14 [4e+06, 4999999] >> >> annotation: >> seq_name id inter_base >> 1 chr14 HIC_bin1 FALSE >> 2 chr14 HIC_bin2 FALSE >> 3 chr14 HIC_bin3 FALSE >> 4 chr14 HIC_bin4 FALSE >> 5 chr14 HIC_bin5 FALSE >> >>> dput hic.gr) >> new("Genome_intervals" >> , .Data = structure(c(1, 1e+06, 2e+06, 3e+06, 4e+06, 999999, >> 1999999, >> 2999999, >> 3999999, 4999999), .Dim = c(5L, 2L)) >> , annotation = structure(list(seq_name = structure(c(1L, 1L, 1L, >> 1L, >> 1L), .Label = "chr14", class = "factor"), >> id = structure(c(1L, 20L, 31L, 42L, 53L), .Label = c("HIC_bin1", >> "HIC_bin10", "HIC_bin100", "HIC_bin101", "HIC_bin102", >> "HIC_bin103", >> "HIC_bin104", "HIC_bin105", "HIC_bin106", "HIC_bin107", >> "HIC_bin11", >> "HIC_bin12", "HIC_bin13", "HIC_bin14", "HIC_bin15", "HIC_bin16", >> "HIC_bin17", "HIC_bin18", "HIC_bin19", "HIC_bin2", "HIC_bin20", >> "HIC_bin21", "HIC_bin22", "HIC_bin23", "HIC_bin24", "HIC_bin25", >> "HIC_bin26", "HIC_bin27", "HIC_bin28", "HIC_bin29", "HIC_bin3", >> "HIC_bin30", "HIC_bin31", "HIC_bin32", "HIC_bin33", "HIC_bin34", >> "HIC_bin35", "HIC_bin36", "HIC_bin37", "HIC_bin38", "HIC_bin39", >> "HIC_bin4", "HIC_bin40", "HIC_bin41", "HIC_bin42", "HIC_bin43", >> "HIC_bin44", "HIC_bin45", "HIC_bin46", "HIC_bin47", "HIC_bin48", >> "HIC_bin49", "HIC_bin5", "HIC_bin50", "HIC_bin51", "HIC_bin52", >> "HIC_bin53", "HIC_bin54", "HIC_bin55", "HIC_bin56", "HIC_bin57", >> "HIC_bin58", "HIC_bin59", "HIC_bin6", "HIC_bin60", "HIC_bin61", >> "HIC_bin62", "HIC_bin63", "HIC_bin64", "HIC_bin65", "HIC_bin66", >> "HIC_bin67", "HIC_bin68", "HIC_bin69", "HIC_bin7", "HIC_bin70", >> "HIC_bin71", "HIC_bin72", "HIC_bin73", "HIC_bin74", "HIC_bin75", >> "HIC_bin76", "HIC_bin77", "HIC_bin78", "HIC_bin79", "HIC_bin8", >> "HIC_bin80", "HIC_bin81", "HIC_bin82", "HIC_bin83", "HIC_bin84", >> "HIC_bin85", "HIC_bin86", "HIC_bin87", "HIC_bin88", "HIC_bin89", >> "HIC_bin9", "HIC_bin90", "HIC_bin91", "HIC_bin92", "HIC_bin93", >> "HIC_bin94", "HIC_bin95", "HIC_bin96", "HIC_bin97", "HIC_bin98", >> "HIC_bin99"), class = "factor"), inter_base = c(FALSE, FALSE, >> FALSE, FALSE, FALSE)), .Names = c("seq_name", "id", "inter_base" >> ), row.names = c(NA, 5L), class = "data.frame") >> , closed = structure(c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, >> TRUE, >> TRUE, >> TRUE), .Dim = c(5L, 2L)) >> , type = "Z" >> ) >> >> [[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 > > _______________________________________________ > 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

Dear Valerie, thanks for answering. This is my session: > library (HiTC) Lade nötiges Paket: girafe Lade nötiges Paket: IRanges Lade nötiges Paket: BiocGenerics Attache Paket: ‘BiocGenerics’ The following object(s) are masked from ‘package:stats’: xtabs The following object(s) are masked from ‘package:base’: anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique Lade nötiges Paket: Rsamtools Lade nötiges Paket: GenomicRanges Lade nötiges Paket: Biostrings Lade nötiges Paket: ShortRead Lade nötiges Paket: lattice Lade nötiges Paket: latticeExtra Lade nötiges Paket: RColorBrewer Lade nötiges Paket: intervals Attache Paket: ‘intervals’ The following object(s) are masked from ‘package:Biostrings’: type The following object(s) are masked from ‘package:GenomicRanges’: reduce The following object(s) are masked from ‘package:IRanges’: expand, reduce Lade nötiges Paket: genomeIntervals Lade nötiges Paket: grid Warnmeldungen: 1: vorhergehender Import ‘coerce’ während des Ladens von ‘intervals’ ersetzt 2: vorhergehender Import ‘initialize’ während des Ladens von ‘intervals’ ersetzt > exDir <- system.file("extdata", package="HiTC") > hC <- import.my5C(file.path(exDir,"HIC_gm06690_chr14_chr14_1000000_obs.txt") ) Convert my5C matrix file in HiTC object(s) Loading chr14-chr14... > detail (hC$chr14chr14) HTC object Focus on genomic region [chr14:1-106368584] Matrix of Interaction data: [107-107] 107 genome intervals from 'xgi' object 107 genome intervals from 'ygi' object Total Reads = 755139 Number of Interactions = 7913 Median Frequency = 30 > hC.gr <- y_intervals (hC$chr14chr14) > hC.gr Object of class Genome_intervals 107 base intervals and 0 inter-base intervals(*): chr14 [1, 999999] chr14 [1e+06, 1999999] chr14 [2e+06, 2999999] chr14 [3e+06, 3999999] ... 99 other intervals... chr14 [1.03e+08, 103999999] chr14 [1.04e+08, 104999999] chr14 [1.05e+08, 105999999] chr14 [1.06e+08, 106368584] annotation: seq_name id inter_base 1 chr14 HIC_bin1 FALSE 2 chr14 HIC_bin2 FALSE 3 chr14 HIC_bin3 FALSE 4 chr14 HIC_bin4 FALSE ... 99 other intervals... seq_name id inter_base 104 chr14 HIC_bin104 FALSE 105 chr14 HIC_bin105 FALSE 106 chr14 HIC_bin106 FALSE 107 chr14 HIC_bin107 FALSE > hC.subset <- hC.gr[1:5,] > dput(hC.subset) new("Genome_intervals" , .Data = structure(c(1, 1e+06, 2e+06, 3e+06, 4e+06, 999999, 1999999, 2999999, 3999999, 4999999), .Dim = c(5L, 2L)) , annotation = structure(list(seq_name = structure(c(1L, 1L, 1L, 1L, 1L), .Label = "chr14", class = "factor"), id = structure(c(1L, 20L, 31L, 42L, 53L), .Label = c("HIC_bin1", "HIC_bin10", "HIC_bin100", "HIC_bin101", "HIC_bin102", "HIC_bin103", "HIC_bin104", "HIC_bin105", "HIC_bin106", "HIC_bin107", "HIC_bin11", "HIC_bin12", "HIC_bin13", "HIC_bin14", "HIC_bin15", "HIC_bin16", "HIC_bin17", "HIC_bin18", "HIC_bin19", "HIC_bin2", "HIC_bin20", "HIC_bin21", "HIC_bin22", "HIC_bin23", "HIC_bin24", "HIC_bin25", "HIC_bin26", "HIC_bin27", "HIC_bin28", "HIC_bin29", "HIC_bin3", "HIC_bin30", "HIC_bin31", "HIC_bin32", "HIC_bin33", "HIC_bin34", "HIC_bin35", "HIC_bin36", "HIC_bin37", "HIC_bin38", "HIC_bin39", "HIC_bin4", "HIC_bin40", "HIC_bin41", "HIC_bin42", "HIC_bin43", "HIC_bin44", "HIC_bin45", "HIC_bin46", "HIC_bin47", "HIC_bin48", "HIC_bin49", "HIC_bin5", "HIC_bin50", "HIC_bin51", "HIC_bin52", "HIC_bin53", "HIC_bin54", "HIC_bin55", "HIC_bin56", "HIC_bin57", "HIC_bin58", "HIC_bin59", "HIC_bin6", "HIC_bin60", "HIC_bin61", "HIC_bin62", "HIC_bin63", "HIC_bin64", "HIC_bin65", "HIC_bin66", "HIC_bin67", "HIC_bin68", "HIC_bin69", "HIC_bin7", "HIC_bin70", "HIC_bin71", "HIC_bin72", "HIC_bin73", "HIC_bin74", "HIC_bin75", "HIC_bin76", "HIC_bin77", "HIC_bin78", "HIC_bin79", "HIC_bin8", "HIC_bin80", "HIC_bin81", "HIC_bin82", "HIC_bin83", "HIC_bin84", "HIC_bin85", "HIC_bin86", "HIC_bin87", "HIC_bin88", "HIC_bin89", "HIC_bin9", "HIC_bin90", "HIC_bin91", "HIC_bin92", "HIC_bin93", "HIC_bin94", "HIC_bin95", "HIC_bin96", "HIC_bin97", "HIC_bin98", "HIC_bin99"), class = "factor"), inter_base = c(FALSE, FALSE, FALSE, FALSE, FALSE)), .Names = c("seq_name", "id", "inter_base" ), row.names = c(NA, 5L), class = "data.frame") , closed = structure(c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE), .Dim = c(5L, 2L)) , type = "Z" ) > sessionInfo() R version 2.15.2 (2012-10-26) Platform: i686-pc-linux-gnu (32-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] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] HiTC_1.2.0 girafe_1.10.0 genomeIntervals_1.14.0 [4] intervals_0.13.3 ShortRead_1.16.3 latticeExtra_0.6-24 [7] RColorBrewer_1.0-5 lattice_0.20-13 Rsamtools_1.10.2 [10] Biostrings_2.26.3 GenomicRanges_1.10.6 IRanges_1.16.4 [13] BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] Biobase_2.18.0 bitops_1.0-5 BSgenome_1.26.1 colorspace_1.2-1 [5] compiler_2.15.2 dichromat_2.0-0 digest_0.6.2 ggplot2_0.9.3 [9] gtable_0.1.2 hwriter_1.3 labeling_0.1 MASS_7.3-23 [13] munsell_0.4 parallel_2.15.2 plyr_1.8 proto_0.3-10 [17] reshape2_1.2.2 scales_0.2.3 stats4_2.15.2 stringr_0.6.2 [21] tools_2.15.2 zlibbioc_1.4.0 > 2013/2/6 Valerie Obenchain <vobencha@fhcrc.org> > Hi Herman, > > When you post a question please provide code that reproduces the problem. > Your example does not show how 'hic.gr' was created or what kind of > object it is. > > library(HiTC) > data(Nora_5C) > intervals <- y_intervals(E14sub) > > The 'intervals' object is a GRanges. > > > class(intervals) > [1] "GRanges" > attr(,"package") > [1] "GenomicRanges" > > You can extract metadata colums with 'mcols'. > > head(mcols(intervals)) > > > head(mcols(intervals)) > DataFrame with 6 rows and 4 columns > name score itemRgb thick > <character> <numeric> <character> <iranges> > 1 FOR_3 0 #0000FF [98834146, 98837506] > 2 FOR_5 0 #0000FF [98840772, 98841227] > 3 FOR_7 0 #0000FF [98843249, 98848364] > 4 FOR_9 0 #0000FF [98849664, 98850577] > 5 FOR_13 0 #0000FF [98862022, 98867230] > 6 FOR_15 0 #0000FF [98869143, 98870524] > > Also use 'mcols' to set the value of a metadata column. > > intervals$newData <- seq_along(intervals) > > head(mcols(intervals)) > DataFrame with 6 rows and 5 columns > name score itemRgb thick newData > <character> <numeric> <character> <iranges> <integer> > 1 FOR_3 0 #0000FF [98834146, 98837506] 1 > 2 FOR_5 0 #0000FF [98840772, 98841227] 2 > 3 FOR_7 0 #0000FF [98843249, 98848364] 3 > 4 FOR_9 0 #0000FF [98849664, 98850577] 4 > 5 FOR_13 0 #0000FF [98862022, 98867230] 5 > 6 FOR_15 0 #0000FF [98869143, 98870524] 6 > > > It looks like y_intervals() is returning a valid GRanges. Can you provide > an example of how you are getting a 'Genome_interval' object? > > Valerie > > > > > On 02/05/2013 01:05 PM, Hermann Norpois wrote: > >> Hello, >> >> in the documentation of HiTC package y_intervals () is described as a >> method to "return the ygi GRanges object defining the y intervals". I >> tried >> this for the test data (see dput) and expected a "classical" GRange >> object. >> For instance I would like to do an operation like >> >> mcols hic.gr)$test<- 1 >> >> But it did not work as hic.gr is a Genome_interval object (as dput >> mentioned). Can I transform this in a classical GR-object allowing >> mcols-operations? Can anybody comment on the difference between >> Genome_interval an Grange? >> >> >> Thanks >> Hermann >> >> >> >> hic.gr >>> >> Object of class Genome_intervals >> 5 base intervals and 0 inter-base intervals(*): >> chr14 [1, 999999] >> chr14 [1e+06, 1999999] >> chr14 [2e+06, 2999999] >> chr14 [3e+06, 3999999] >> chr14 [4e+06, 4999999] >> >> annotation: >> seq_name id inter_base >> 1 chr14 HIC_bin1 FALSE >> 2 chr14 HIC_bin2 FALSE >> 3 chr14 HIC_bin3 FALSE >> 4 chr14 HIC_bin4 FALSE >> 5 chr14 HIC_bin5 FALSE >> >> dput hic.gr) >>> >> new("Genome_intervals" >> , .Data = structure(c(1, 1e+06, 2e+06, 3e+06, 4e+06, 999999, 1999999, >> 2999999, >> 3999999, 4999999), .Dim = c(5L, 2L)) >> , annotation = structure(list(seq_name = structure(c(1L, 1L, 1L, 1L, >> 1L), .Label = "chr14", class = "factor"), >> id = structure(c(1L, 20L, 31L, 42L, 53L), .Label = c("HIC_bin1", >> "HIC_bin10", "HIC_bin100", "HIC_bin101", "HIC_bin102", "HIC_bin103", >> "HIC_bin104", "HIC_bin105", "HIC_bin106", "HIC_bin107", "HIC_bin11", >> "HIC_bin12", "HIC_bin13", "HIC_bin14", "HIC_bin15", "HIC_bin16", >> "HIC_bin17", "HIC_bin18", "HIC_bin19", "HIC_bin2", "HIC_bin20", >> "HIC_bin21", "HIC_bin22", "HIC_bin23", "HIC_bin24", "HIC_bin25", >> "HIC_bin26", "HIC_bin27", "HIC_bin28", "HIC_bin29", "HIC_bin3", >> "HIC_bin30", "HIC_bin31", "HIC_bin32", "HIC_bin33", "HIC_bin34", >> "HIC_bin35", "HIC_bin36", "HIC_bin37", "HIC_bin38", "HIC_bin39", >> "HIC_bin4", "HIC_bin40", "HIC_bin41", "HIC_bin42", "HIC_bin43", >> "HIC_bin44", "HIC_bin45", "HIC_bin46", "HIC_bin47", "HIC_bin48", >> "HIC_bin49", "HIC_bin5", "HIC_bin50", "HIC_bin51", "HIC_bin52", >> "HIC_bin53", "HIC_bin54", "HIC_bin55", "HIC_bin56", "HIC_bin57", >> "HIC_bin58", "HIC_bin59", "HIC_bin6", "HIC_bin60", "HIC_bin61", >> "HIC_bin62", "HIC_bin63", "HIC_bin64", "HIC_bin65", "HIC_bin66", >> "HIC_bin67", "HIC_bin68", "HIC_bin69", "HIC_bin7", "HIC_bin70", >> "HIC_bin71", "HIC_bin72", "HIC_bin73", "HIC_bin74", "HIC_bin75", >> "HIC_bin76", "HIC_bin77", "HIC_bin78", "HIC_bin79", "HIC_bin8", >> "HIC_bin80", "HIC_bin81", "HIC_bin82", "HIC_bin83", "HIC_bin84", >> "HIC_bin85", "HIC_bin86", "HIC_bin87", "HIC_bin88", "HIC_bin89", >> "HIC_bin9", "HIC_bin90", "HIC_bin91", "HIC_bin92", "HIC_bin93", >> "HIC_bin94", "HIC_bin95", "HIC_bin96", "HIC_bin97", "HIC_bin98", >> "HIC_bin99"), class = "factor"), inter_base = c(FALSE, FALSE, >> FALSE, FALSE, FALSE)), .Names = c("seq_name", "id", "inter_base" >> ), row.names = c(NA, 5L), class = "data.frame") >> , closed = structure(c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, >> TRUE, >> TRUE, >> TRUE), .Dim = c(5L, 2L)) >> , type = "Z" >> ) >> >> [[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=""> >> > > [[alternative HTML version deleted]]