Dear list, I would like to have a look at the code of summarizeOverlaps, so I compute: library(GenomicFeatures) showMethods("summarizeOverlaps",includeDefs = T) Function: summarizeOverlaps (package GenomicRanges) features="GRanges", reads="GappedAlignments" function (features, reads, mode = Union, ignore.strand = FALSE, ..., param = ScanBamParam()) { mode <- match.fun(mode) counts <- .dispatch(reads, features, mode, ignore.strand) if (length(metadata(reads)) > 0) colData <- DataFrame(metaData = metadata(reads)) else colData <- DataFrame(metaData = character(1)) SummarizedExperiment(assays = SimpleList(counts = as.matrix(counts)), rowData = features, colData = colData) } features="GRangesList", reads="GappedAlignments" function (features, reads, mode = Union, ignore.strand = FALSE, ..., param = ScanBamParam()) { mode <- match.fun(mode) counts <- .dispatch(reads, features, mode, ignore.strand) if (length(metadata(reads)) > 0) colData <- DataFrame(metaData = metadata(reads)) else colData <- DataFrame(metaData = character(1)) SummarizedExperiment(assays = SimpleList(counts = as.matrix(counts)), rowData = features, colData = colData) } What is .dispatch exactly doing here? How is it working? How can I have a look at the underlying code? Best, Stefanie

On Wed, Mar 28, 2012 at 5:48 AM, Stefanie <stefanie.tauber@univie.ac.at>wrote: > Dear list, > > I would like to have a look at the code of summarizeOverlaps, > so I compute: > > library(GenomicFeatures) > showMethods("summarizeOverlaps",includeDefs = T) > > Function: summarizeOverlaps (package GenomicRanges) > features="GRanges", reads="GappedAlignments" > function (features, reads, mode = Union, ignore.strand = FALSE, > ..., param = ScanBamParam()) > { > mode <- match.fun(mode) > counts <- .dispatch(reads, features, mode, ignore.strand) > if (length(metadata(reads)) > 0) > colData <- DataFrame(metaData = metadata(reads)) > else colData <- DataFrame(metaData = character(1)) > SummarizedExperiment(assays = SimpleList(counts = as.matrix(counts)), > rowData = features, colData = colData) > } > > > features="GRangesList", reads="GappedAlignments" > function (features, reads, mode = Union, ignore.strand = FALSE, > ..., param = ScanBamParam()) > { > mode <- match.fun(mode) > counts <- .dispatch(reads, features, mode, ignore.strand) > if (length(metadata(reads)) > 0) > colData <- DataFrame(metaData = metadata(reads)) > else colData <- DataFrame(metaData = character(1)) > SummarizedExperiment(assays = SimpleList(counts = as.matrix(counts)), > rowData = features, colData = colData) > } > > What is .dispatch exactly doing here? How is it working? How can I have a > look > at the underlying code? > > GenomicRanges:::.dispatch function (reads, features, mode, ignore.strand, ...) { if (ignore.strand) strand(reads) <- "*" mode(reads, features, ignore.strand) } <environment: namespace:genomicranges=""> > Best, > Stefanie > > _______________________________________________ > 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]]

Hi Stefanie, On Wed, Mar 28, 2012 at 5:48 AM, Stefanie <stefanie.tauber at="" univie.ac.at=""> wrote: > Dear list, > > I would like to have a look at the code of summarizeOverlaps, > so I compute: > > library(GenomicFeatures) > showMethods("summarizeOverlaps",includeDefs = T) [snip] If you really want to dig into the code to figure out what's going on, I'd recommend that you download the *source* GenomicRanges package (and IRanges, for that matter) and start hunting ... it's a bit of work, but will likely be a good learning experience. -steve -- 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

Hi, thanks. I know downloading the source would state the most complete choice. I just wanted to know how to have a quick look in R... Thanks for your answers!! Best, Stefanie