User: FDG

gravatar for FDG
FDG70
Reputation:
70
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New User
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Last seen:
3 months, 4 weeks ago
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7 months ago
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Posts by FDG

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Comment: C: maintainer option for bioconductor packages
... again, I was just wondering, there is no need to react so violently. I now understand its mostly volenteer work, so again I thank you for your answer ...
written 6 months ago by FDG70
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Comment: C: maintainer option for bioconductor packages
... the email in question (which said it could not be delivered) went to the spam box, and that is why I just noticed. I was just wondering how packages are being maintained, and of course a google search could possibly have solved this, if the question wasn't solved already. I do believe however that i ...
written 6 months ago by FDG70
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maintainer option for bioconductor packages
... How is the maintainer("packagename") maintained by Bioconductor? Because I couldn't reach the maintainer via this webforum, but also I could not reach him/her using the maintainer() option. When I tried to use the e-mail address provided with this option I got:  " Mail Delivery System - I'm sorry to ...
R bioconductor written 6 months ago by FDG70 • updated 6 months ago by James W. MacDonald50k
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Comment: C: RSVSim insertions from chr1 to chr2
... o make this customizable change: sizes <- c(whatever, numbers, you, like) output=NA (to a file path prefix to get a .csv file with the metadata) genome = DNAStringSet() To replace the sample sequence bpSeqSize = number (to change how many of the flanking region is shown in the metadata) ...
written 6 months ago by FDG70
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Answer: A: RSVSim insertions from chr1 to chr2
... Finally found a solution based on RSVSim genome = DNAStringSet( c(chr1 = "AAAAAAAAAAAAAAAAAAAATTTTTTTTTTTTTTTTTTTT", chr2 = "GGGGGGGGGGGGGGGGGGGGCCCCCCCCCCCCCCCCCCCC")) length_seq_chr1 = width(genome[1]) - 10 length_seq_chr2 = width(genome[2]) - 10 sizes <- c( ...
written 6 months ago by FDG70
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Comment: C: RSVSim insertions from chr1 to chr2
... I think I got it now. Do you see any problems in this code? genome = DNAStringSet( c(chr1 = "AAAAAAAAAAAAAAAAAAAATTTTTTTTTTTTTTTTTTTT", chr2 = "GGGGGGGGGGGGGGGGGGGGCCCCCCCCCCCCCCCCCCCC")) sampleFromGenome <- function(genome, wd) { chrProb <- width(genome) / sum(width(genome)) chr ...
written 6 months ago by FDG70
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Comment: C: RSVSim insertions from chr1 to chr2
... I looked at what you wrote, and it almost seems to do the trick. The problem is that the output is now still the same as with simulateSV. Sometimes the insertion is in chr1 and sometimes in chr2. I really need it to go from chr1 --> chr2 (the deletions don't even matter, but that was something th ...
written 6 months ago by FDG70
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Comment: C: RSVSim insertions from chr1 to chr2
... Sorry for the late reply. I will try this out today. thanks again for the help ...
written 6 months ago by FDG70
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Comment: C: RSVSim insertions from chr1 to chr2
... While it does give the desired result in the example, it does not give me the desired result overall. So now my code is: library(Biostrings) library(GenomicRanges) genome = DNAStringSet( c(chr1 = "AAAAAAAAAAAAAAAAAAAATTTTTTTTTTTTTTTTTTTT", chr2 = "GGGGGGGGGGGGGGGGGGGGCCCCCCCCCCCCCCCCCCCC")) ...
written 6 months ago by FDG70
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Comment: C: RSVSim insertions from chr1 to chr2
... I will have a look into it, thanks for the reply! Now it doesn't seem to be at random places though, but that is something I can implement later. I let you know how it goes. ...
written 6 months ago by FDG70

Latest awards to FDG

Scholar 7 months ago, created an answer that has been accepted. For A: RSVSim insertions from chr1 to chr2
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: RSVSim insertions from chr1 to chr2

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