User: hauken_heyken
hauken_heyken • 40
- Reputation:
- 40
- Status:
- New User
- Location:
- Last seen:
- 5 hours ago
- Joined:
- 7 months, 1 week ago
- Email:
- h************@hotmail.com
Posts by hauken_heyken
<prev
• 30 results •
page 1 of 3 •
next >
0
votes
1
answers
58
views
1
answers
... 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_heyken • 40
1
vote
1
answer
58
views
1
answer
... 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 5 days ago by
hauken_heyken • 40
0
votes
1
answers
65
views
1
answers
... 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_heyken • 40
1
vote
1
answer
65
views
1
answer
... 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 7 weeks ago by
hauken_heyken • 40
• updated 7 weeks ago by
Martin Morgan ♦♦ 21k
0
votes
3
answers
696
views
3
answers
... 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_heyken • 40
0
votes
0
answers
149
views
0
answers
... In more simple terms, what I am saying is:
How do you allow negative widths on IRanges ?
...
written 4 months ago by
hauken_heyken • 40
0
votes
0
answers
149
views
0
answers
... 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 4 months ago by
hauken_heyken • 40
0
votes
2
answers
332
views
2
answers
... 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_heyken • 40
0
votes
2
answers
213
views
2
answers
... 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_heyken • 40
0
votes
2
answers
213
views
2
answers
... 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_heyken • 40
Latest awards to hauken_heyken
No awards yet. Soon to come :-)
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.2.0
Traffic: 326 users visited in the last hour