User: hauken_heyken
hauken_heyken • 50
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Posts by hauken_heyken
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... 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 14 days ago by
hauken_heyken • 50
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... 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 12 months ago by
hauken_heyken • 50
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... 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 ...
written 12 months ago by
hauken_heyken • 50
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... 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 13 months ago by
hauken_heyken • 50
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... 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 ...
written 13 months ago by
hauken_heyken • 50
• updated
13 months ago by
Martin Morgan ♦♦ 23k
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... 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 14 months ago by
hauken_heyken • 50
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... In more simple terms, what I am saying is:
How do you allow negative widths on IRanges ?
...
written 16 months ago by
hauken_heyken • 50
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... 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 ...
written 16 months ago by
hauken_heyken • 50
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... 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 17 months ago by
hauken_heyken • 50
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... 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 17 months ago by
hauken_heyken • 50
Latest awards to hauken_heyken
Scholar
19 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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