User: ioannis.vardaxis

Reputation:
30
Status:
New User
Location:
Norway/Trondheim/NTNU
Last seen:
3 months, 2 weeks ago
Joined:
2 years, 8 months ago
Email:
i***************@ntnu.no

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 3 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 3 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 3 months ago by ioannis.vardaxis30 • updated 3 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 16 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 16 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 16 months ago by ioannis.vardaxis30 • updated 16 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 16 months ago by ioannis.vardaxis30 • updated 16 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 16 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 16 months ago by ioannis.vardaxis30 • updated 16 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 20 months ago by ioannis.vardaxis30

Latest awards to ioannis.vardaxis

Scholar 2.1 years ago, created an answer that has been accepted. For A: Reading fastq file after narrowing sequences

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