search for: rsamtools

Hi all: I've got a data of ".bam" which is created from my partner under linux sysyem. My system is window xp, and I wanna know how to read the .bam file. Many thanks! My best [[alternative HTML version deleted]]

...in that example using `mclapply` and so it is significantly faster than other alternatives. It is a very simple and contrived example, but there are lots of applications that depend on processing of large data and benefit from multithreading. For example, if I read in large sequencing data with `Rsamtools` and want to check sequences for a set of motifs. > I don't see why mclapply could not be rewritten using PSOCK clusters. Because it would be much slower. > To implement copy-on-write, Linux overcommits virtual memory, and this > is what causes scripts to break unexpectedly: everyt...

...t (which includes the code. Below is a transcript of my R session. First I load the code from a file, using source(). Then I execute it fine. Then I remove the function object, I load the package, and execute the same code from the package - and I get an error. Please help! Mick > library(Rsamtools) > source("viRome/R/read.bam.R") > read.bam function(bamfile=NULL, chr=NULL, start=1, end=1e07, what=c("qname", "flag", "rname", "strand", "pos", "qwidth", "mapq", "cigar", "mrnm",...

Hello everyone. There is a new competition, outlined on the blog dataists<http://www.dataists.com/2010/10/using-data-tools-to-find-data-tools-the-yo-dawg-of-data-hacking/>, inviting us to analyse statistics of the use of R packages (collected from 52 R users), to create a R-package suggestion engine for ourselves. Since I noticed several bloggers already wrote about it (as I have detailed

...ply` and so it is significantly faster than other > alternatives. > > It is a very simple and contrived example, but there are lots of > applications that depend on processing of large data and benefit from > multithreading. For example, if I read in large sequencing data with > `Rsamtools` and want to check sequences for a set of motifs. > > > I don't see why mclapply could not be rewritten using PSOCK clusters. > > Because it would be much slower. > > > To implement copy-on-write, Linux overcommits virtual memory, and this > > is what causes scrip...

Just throwing my two cents in: I think removing/deprecating fork would be a bad idea for two reasons: 1) There are no performant alternatives 2) Removing fork would break existing workflows Even if replaced with something using the same interface (e.g., a function that automatically detects variables to export as in the amazing `future` package), the lack of copy-on-write functionality would

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