User: felix.ernst

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Posts by felix.ernst

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Using non standard charachters with XStrings object in BioStrings
... How about the `Modstrings` package? That is basically the functionality, just with special characters. So if one could define a new dictionary for this purpose as done in the `Modstrings`. ...
written 4 months ago by felix.ernst0
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Comment: C: DataFrame matrix subsetting
... Hi Herve, thanks for the answer. I will look into opening an issue. Felix ...
written 8 months ago by felix.ernst0
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DataFrame matrix subsetting
... Hi all, I am not sure, whether this example should work or works as intended df <- DataFrame(one = c(1,2,3), two = c(NA,NA,NA)) df[is.na(df)] Error: subscript is a logical vector with out-of-bounds TRUE values In addition: Warning message: In NSBS(i, x, exact = exact, strict ...
s4vectors subsetting dataframe written 9 months ago by felix.ernst0 • updated 9 months ago by Hervé Pagès ♦♦ 14k
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alphabet/encoding IlluminaQuality SolexaQuality
... Hi, I am bit new to using XStringQuality information. However I noticed, that encoding() and alphabet() return NA values for values not included in the Illumina/Solexa scores. The manual says values between 0:99/-5:99 are accepted. How should this be interpreted? Do the classes follow current enco ...
biostrings xstringquality written 11 months ago by felix.ernst0
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Answer: A: rtracklayer demo bug
... Thanks a lot.   ...
written 19 months ago by felix.ernst0
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rtracklayer demo bug
... Hello, does anyone else have a problem using demo(targets) to have a look at the example in the rtracklayer package? The error is given after chunk 6 > view <- browserView(session, range, + hide = c("refGene", "mgcFullMrna", "intronEst"), + dense = " ...
rtracklayer written 19 months ago by felix.ernst0
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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 20 months 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 20 months 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 20 months 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 20 months ago by felix.ernst0 • updated 20 months ago by Michael Lawrence11k

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