User: hauken_heyken

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Posts by hauken_heyken

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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 7 weeks 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 7 weeks 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 9 weeks 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 9 weeks 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 10 weeks ago by hauken_heyken40
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Comment: A: How to filter all column using Loop
... Do you want all positions with < 5 to be replaced by NA values ? ...
written 10 weeks ago by hauken_heyken40
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Comment: C: How to construct a valid GRanges object from RCPP and pass back to R
... BTW: This produces an error in package creation with devtools, do you know how to fix it: I put this in an cpp file: Environment envGenomicRanges("package:GenomicRanges"); Function GRanges = envGenomicRanges["GRanges"]; Then the namespace file contains this one, and more: import(GenomicRanges) ...
written 10 weeks ago by hauken_heyken40
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Comment: C: Accessing GRangesList rows in Rcpp
... This will work, and make it a lot easier, and more like how C++ should be, since I'm polluting my code with a lot of R API right now, which makes it slower I think. Thank you, I will accept your answer. Another point you make that is important, is that if you vectorize R code efficiently, then it ...
written 11 weeks ago by hauken_heyken40
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Comment: C: Accessing GRangesList rows in Rcpp
... I'm thinking about the simple vector possibility, but I still need a grouped vector by transcripts, makes it harder.. i.g if grangeslist have 2 transcript with two exons each, I would need to make a class or something for this, would be easier to use GRangesList API if it exists.. ...
written 11 weeks ago by hauken_heyken40
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Comment: C: Accessing GRangesList rows in Rcpp
... This is not my goal, it's only a part of the program, my whole program takes a GRangeslist and fastaSequences, and returns a GRangesList with all orfs of the original GRangeslist. I need this to access each GRangesList by transcript ...
written 11 weeks ago by hauken_heyken40

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