User: Arne Muller

gravatar for Arne Muller
Arne Muller20
Reputation:
20
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New User
Location:
United States
Last seen:
1 year, 5 months ago
Joined:
2 years, 4 months ago
Email:
a**********@gmail.com

Posts by Arne Muller

<prev • 10 results • page 1 of 1 • next >
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slow granges in GAlignmentPairs
... Hello, I'm trying to extract the position and fragment length of paired end reads from bam files using readGAlignmentPairs and granges. There was already a posting (https://support.bioconductor.org/p/60339/) about the performance of readGAlignmentPairs, but another issue is that the granges method ...
genomicalignments written 18 months ago by Arne Muller20 • updated 17 months ago by Hervé Pagès ♦♦ 13k
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MedIP-Seq: IP over Input with edgeR
... Hello, I'd like to run edgeR on a MeDIP-Seq experiment with 4 treatment groups (each with 5 samples). I'm counting reads in slides over the genome (a few hundred bases with some overlap). I realised that there is a small batch effect as both IP and input separates per treatment group in an MDS plo ...
edge written 2.1 years ago by Arne Muller20 • updated 2.1 years ago by Aaron Lun17k
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Answer: A: Problem installing BSgenome.Hsapiens.UCSC.hg19
... Hi. The BSgenome package has a dependency on the XML package (via rtracklayer). The XML package itself depends on the system library libxml2 which must be installed in your system with version 2.6.3 or higher. On my old Linux redhat system the library were too old. I can give hints how to solve this ...
written 2.1 years ago by Arne Muller20
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Comment: C: readGAlignments + BamViews not working in BioC-Devel
... Hi - I think there's still a problem. Bioc-Release still uses 1.2.9 whereas in the svn there's' already 1.2.18 for release (note, the build/check report says there's a timeout for 1.2.18). ...
written 2.3 years ago by Arne Muller20
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estimateCellCounts: proportions and sex
... Hello, I am using the estimateCellCounts function that implements the Houseman regression to estimate blood cell types in Infinium 450k data derived from blood. As far as I understand this is a quadratic programming method that constraints the estimates to sum up to 1 per sample, but in my dataset ...
minfi written 2.3 years ago by Arne Muller20 • updated 21 months ago by Chi Hong0
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Answer: A: readGAlignments + BamViews not working in BioC-Devel
... Hi - thanks for this fix in Rsamtools, but this only fixes the problem in one place, there's another (and possibly more) in GenomicAlignments::summarizeOverlaps: mapq_filter <- function(features, reads, algorithm, ignore.strand, inter.feature) { re ...
written 2.3 years ago by Arne Muller20 • updated 2.3 years ago by Martin Morgan ♦♦ 20k
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Answer: A: readGAlignments + BamViews not working in BioC-Devel
... Hi - the error also occurs with R-3.2.0 and BiocDevel: aln <- readGAlignments(bv) Error in readGAlignments(bv) : Assertion on 'more.args' failed: Vector must be named Enter a frame number, or 0 to exit 1: readGAlignments(bv) 2: readGAlignments(bv) 3: Rsamtools:::.BamViews_delegate("r ...
written 2.4 years ago by Arne Muller20 • updated 2.4 years ago by Martin Morgan ♦♦ 20k
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readGAlignments + BamViews not working in BioC-Devel
... Hi All, I'm wondering why the code below throws an error. I'm using R-devel (3.3.0) + BioC-devel. Is this a bug or did I miss something. From the GenomicAlignments help: ## With a BamViews object: fls <- system.file("extdata", "ex1.bam", package="Rsamtools", mustWork=TRUE) ...
rsamtools genomicalignments written 2.4 years ago by Arne Muller20
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csaw: input coverage RleLists instead of bam files
... Hello, would it be possible+reasonable to enter csaw peak calling with RleLists objects such as those generated by the GenomicAlignments' coverage method? I guess it'd be more performant to store and load the RleList objects compared to bam files. As I understand the coverage vector + the available ...
csaw written 2.4 years ago by Arne Muller20 • updated 2.4 years ago by Aaron Lun17k
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FastqSampler with trimmed paired-end reads
... Hello, I came across a problems with FastqSampler from the ShortRead package. I get non-matching pairs/mates (reads that don;t belong to each other)  when doing: f1 <- FastqSampler("file1.fastq", n=1e6) f2 <- FastqSampler("file2.fastq", n=1e6) set.seed(123L); p1 <- yield(f1) set.seed(12 ...
shortread written 2.4 years ago by Arne Muller20 • updated 2.4 years ago by Martin Morgan ♦♦ 20k

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