User: ioannis.vardaxis

Reputation:
30
Status:
New User
Location:
Norway/Oslo
Last seen:
3 weeks, 3 days ago
Joined:
2 years, 10 months ago
Email:
i*****@hotmail.com

Posts by ioannis.vardaxis

<prev • 19 results • page 1 of 2 • next >
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Comment: C: Convert BAM to FASTQ
... Thank you ! This did the job :) ...
written 5 months ago by ioannis.vardaxis30
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Comment: C: Convert BAM to FASTQ
... Thanks, but I need it in R since it is part of my R-package :/ ...
written 5 months ago by ioannis.vardaxis30
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Convert BAM to FASTQ
... Hey, In my package I was using rbamtools from CRAN for converting some BAM files to FASTQ. However rbamtools is now depressed, so I was wondering if there is any function in Bioconductor which can do that. I tried to find it myself with no luck. Best, ...
bam fastq written 5 months ago by ioannis.vardaxis30 • updated 5 months ago by Martin Morgan ♦♦ 23k
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Comment: C: Disable messages for bplapply when in parallel
... Perfect! Thanks for the help! ...
written 18 months ago by ioannis.vardaxis30
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Comment: C: Disable messages for bplapply when in parallel
... I tried suppressPackageStartupMessages(library(YourPackage)) inside the function I call in parallel but I still get the messages. Link to my package: https://bioconductor.org/packages/devel/bioc/html/MACPET.html Now this version also runs bplapply() but not in a loop (the loop is prepared for ...
written 18 months ago by ioannis.vardaxis30
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Comment: C: Disable messages for bplapply when in parallel
... I am on MAC and I register the snow workers like the following: snow <- BiocParallel::SnowParam(workers = 4, type = 'SOCK', progressbar=FALSE) BiocParallel::register(snow, default=TRUE) I tried bpstart/bpstop but the messages are still printed every time the loop is run. I tested the followin ...
written 18 months ago by ioannis.vardaxis30 • updated 18 months ago by Martin Morgan ♦♦ 23k
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Disable messages for bplapply when in parallel
... Hey, I have a simple question. I am using  the BiocParallel::bplapply in a package I am building, and the function runs in parallel. However every time the function will start running I get the following messages: Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery. ...
biocparallel bplapply written 18 months ago by ioannis.vardaxis30 • updated 18 months ago by Martin Morgan ♦♦ 23k
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Comment: C: BiocParallel NULL value passed as symbol address
... Hey, I did as you suggested. If I source the Rcpp code in the loop it works, but it takes a lot of time and I need to check if it is worth running it in parallel. If on the other hand I place the Rcpp code in my pkg and try to run it this way I get the following error: Error in .Call("_pkg_Testi ...
written 18 months ago by ioannis.vardaxis30
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BiocParallel NULL value passed as symbol address
... Hey, I have written a simple function Rcpp package, the function is the following: #include <Rcpp.h> using namespace Rcpp; //[[Rcpp::export]] SEXP Test(double &i){ double j=std::pow(i,2.0); return Rcpp::wrap(j); } I can source the code and run the function Test. But I want to ...
biocparallel rcpp written 18 months ago by ioannis.vardaxis30 • updated 18 months ago by Martin Morgan ♦♦ 23k
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Answer: A: Reading fastq file after narrowing sequences
... I solved it. I also had to narrow the qualities slot in the fastq file before saving. Now it uploads just fine. ...
written 22 months ago by ioannis.vardaxis30

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Scholar 2.3 years ago, created an answer that has been accepted. For A: Reading fastq file after narrowing sequences

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