User: hauken_heyken

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Posts by hauken_heyken

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Rsubread, Error in featureCounts paired end
... Hey, nice package. I have an error using featureCounts with paired end reads: I mapped paired end reads with STAR (trimmed reads with fastp), and wanted to try out Rsubread to do the counting in R. library(Rsubread) # Define paths to RNA-seq bam file and gtf a <- featureCounts(file ...
rsubread featurecounts paired end written 6 weeks ago by hauken_heyken • 60 • updated 4 weeks ago by Wei Shi • 3.1k
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Answer: A: invalid class GRanges object: 1: 'x@seqnames' is not parallel to 'x
... Funny thing is that if you switch the second number by +1, it works: Try: GRanges(c("chr1", "chr1", "chr1"), c(109810200, 109810202, 109810544)) # 202, instead of 201 If you write ?GRanges, you see the ranges argument if defined as: IRanges, or single integer range, where integer values next ...
written 4 months ago by hauken_heyken • 60
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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 16 months ago by hauken_heyken • 60
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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 16 months ago by hauken_heyken • 60
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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 17 months ago by hauken_heyken • 60
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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 17 months ago by hauken_heyken • 60 • updated 17 months ago by Martin Morgan ♦♦ 23k
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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 18 months ago by hauken_heyken • 60
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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 20 months ago by hauken_heyken • 60
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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 20 months ago by hauken_heyken • 60
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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 21 months ago by hauken_heyken • 60

Latest awards to hauken_heyken

Popular Question 8 months ago, created a question with more than 1,000 views. For How to construct a valid GRanges object from RCPP and pass back to R
Scholar 23 months ago, created an answer that has been accepted. For A: Subsetting Rle with ORF-sequence-positions by the 3 frames
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