User: hauken_heyken

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Posts by hauken_heyken

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Answer: A: Subsetting Rle with ORF-sequence-positions by the 3 frames
... Ok, will answer this one my self. I found a sufficient answer, which uses S4Vectors math operators. A very fast way to find which frame a read hit is on in a big RleList: This example finds the frame of  the read in all ORFs with only 1 hit. cov # the Rle sum(runLength(cov)[(cumsum(runValue(co ...
written 7 hours ago by hauken_heyken40
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Subsetting Rle with ORF-sequence-positions by the 3 frames
... I have a list of 4.5 million orfs, so I need a fast method for this. Right now the function uses 0.1 terabyte of RAM  per core, which I think is way too much. (2 terabyte server) So I can only run  20 processes at a time.   Here is the problem: First I get the coverage of ribo-seq per ORF. Let ...
rle big data coveragebytranscript written 5 days ago by hauken_heyken40
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Comment: C: extending GenomicRanges::reduce warning, why ?
... Thanks for the help Martin, slowly learning the way of R.   I renamed the function to reduce_keep_attr It tries to keep the meta columns and naming if it makes sense after reduction. ...
written 7 weeks ago by hauken_heyken40
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extending GenomicRanges::reduce warning, why ?
... Ok, so I want my own definition of reduce, that calls GenomicRanges::reduce() if keep.names = F, the extra argument I want. I can not find the original setGeneric for reduce, I guess it's auto-created ? my generic is: setGeneric("reduce", function(x, ...) standardGeneric("reduce")) # i extend wi ...
genomicranges reduce setmethod setgeneric written 7 weeks ago by hauken_heyken40 • updated 7 weeks ago by Martin Morgan ♦♦ 21k
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Answer: A: Upgrade bioconductor 3.2 to 3.3
... This will work for everyone on both servers and local, as long as you can install local user files. 1: Go to biocinstaller page, and download the .tar file: https://bioconductor.org/packages/release/bioc/html/BiocInstaller.html 2.  in R, create a new session and do: remove.packages("BiocInstalle ...
written 12 weeks ago by hauken_heyken40
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Comment: C: Rcpp adding circular ranges to GRanges object in c++
... In more simple terms, what I am saying is: How do you allow negative widths on IRanges ? ...
written 4 months ago by hauken_heyken40
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Rcpp adding circular ranges to GRanges object in c++
... Hey, I have the circular Ecoli genome, and I want to construct a GRanges object of all ORFs in the fasta file from ncbi.   I made a c++ function to do it, but of course since some of the orfs that starts just before the stop of the genome, and ends after the start, will make IRanges() constructor ...
iranges granges rcpp circular written 4 months ago by hauken_heyken40
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Comment: C: How to construct a valid GRanges object from RCPP and pass back to R
... CORRECTION!!: This is the way to do it safely Function GRanges("GRanges", Environment::namespace_env("GenomicRanges")); You can not do: Environment envGenomicRanges("package:GenomicRanges"); Because it will screw up the namespace if used in packages. ...
written 5 months ago by hauken_heyken40
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Comment: C: How to filter all column using Loop
... Ah, okey, now it makes sence. Then this will work: New version is: library(data.table) b=c(1,2,3,4,5,8,10) c=c(1,2,3,4,6,7,10) e=c(1,2,10,5,12,15,10) d = as.data.table(cbind(b,c,e)) indexesToRemove = lapply(1:ncol(d),function(x) ifelse(d[,as.integer(x), with = F] >= 5,as.integer(x), NA )) ...
written 5 months ago by hauken_heyken40
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Answer: A: How to filter all column using Loop
... I dont know if I understand your question correctly, but this will work, if you want to only keep columns with rows >= 5:   library(data.table) a = c(1,2,3,4,5) b = c(4,5,6,7,8) c = c(6,7,8,9,10) e = c(1,2,3,4,4) # <--- This column will be filtered out, because non is >= 5 d = as.data ...
written 5 months ago by hauken_heyken40

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