User: felix.ernst

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Posts by felix.ernst

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Comment: C: intronsByTranscript and fiveUTRsByTranscript - not recognized annotations
... TxDb expects UTR regions to be included in the exon annotation. Reminder: exon != CDS ...
written 17 days ago by felix.ernst0
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Comment: C: intronsByTranscript and fiveUTRsByTranscript - not recognized annotations
... Thanks Michael. I checked again, You are right :/ :( ...
written 17 days ago by felix.ernst0
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Comment: C: intronsByTranscript and fiveUTRsByTranscript - not recognized annotations
... > exonsBy(txdb) GRangesList object of length 1: $1 GRanges object with 2 ranges and 3 metadata columns: seqnames ranges strand | exon_id exon_name exon_rank <Rle> <IRanges> <Rle> | <integer> <character> <integer> [1] chr ...
written 17 days ago by felix.ernst0
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(Closed) intronsByTranscript and fiveUTRsByTranscript - not recognized annotations
... Hi, I am having a bit of trouble to get the introns and exons from a transcript. Have a look at this snippet. library(GenomicFeatures) file <- "test.gff3" print(readLines(file)) txdb <- makeTxDbFromGFF(file) print(transcripts(txdb)) print(intronsByTranscript(txdb)) print(fiveUTRsByTranscr ...
genomicfeatures written 17 days ago by felix.ernst0 • updated 17 days ago by Michael Lawrence9.9k
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seqnames versus chrom
... Dear all, I can retrieve the chromosome names stored in a GRanges object either using GenomeInfoDb::seqnames() or rtracklayer::chrom(). This deviates from the use of the other accessor functions, such as BiocGenerics::start(), BiocGenerics::end(), etc Is there a reason for this split up? Is there ...
rtracklayer genomeinfodb biocgen written 5 weeks ago by felix.ernst0 • updated 5 weeks ago by Michael Lawrence9.9k
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Comment: C: Correct way to load a package inside bplapply function
... Sorry, forgot that. I update the sessionInfo output in the original thread opening post, since there is a 5000 character limit for replies. ​the dependencies can be installed using this: source("https://bioconductor.org/biocLite.R") biocLite() biocLite("devtools") devtools::find_rtools() library(de ...
written 6 months ago by felix.ernst0
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Comment: C: Correct way to load a package inside bplapply function
... addition because of the 5000 spaces limit: The output is of course much shorter and for each file loaded the output appears: <environment: namespace:base> cpu elapsed transient class <environment: namespace:tools> ...
written 6 months ago by felix.ernst0
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Comment: C: Correct way to load a package inside bplapply function
... The problem exists with 3.4.1 in a fresh install as well. The example function does not return a output, so the problem has to be in connection with some thing else. Therefore I modified the function stepwise and commented out all the function calls and simplified some stuff so I ended up with this ...
written 6 months ago by felix.ernst0
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Comment: C: Correct way to load a package inside bplapply function
...   Thanks for the advice. I will do that in the next couple of days. I tried updating to R 3.4.0 a couple of month ago, but couldn't do it, since some dependencies were not up to date. What is your comment on the usage of loadNamespace vs requireNamespace? The function in question with the weird ou ...
written 6 months ago by felix.ernst0
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Comment: C: Correct way to load a package inside bplapply function
... Hi Martin, I did so more digging. It looks to me that this might be an output, which one could get from selectMethod   seqinfo check.names seqnames ranges strand mcols seqlengths seqinfo <envir ...
written 6 months ago by felix.ernst0

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