User: ben.ward

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ben.ward30
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United Kingdom
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1 year, 8 months ago
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2 years, 11 months ago
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b*******@sainsbury-laboratory.ac.uk

Posts by ben.ward

<prev • 14 results • page 1 of 2 • next >
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IRanges, Partitioning by End function not found.
... Hi, in my package I have a method which subsets a DNAStringSet:   setGeneric("subsetSites", function(object, index){ standardGeneric("subsetSites") } ) setMethod("subsetSites", signature("DNAStringSet", "integer"), function(object, index){ ...
biostrings iranges written 22 months ago by ben.ward30 • updated 22 months ago by Martin Morgan ♦♦ 20k
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Answer: A: custom iterators and foreach inside package - fails
... I've managed to solve this. In order for foreach to work inside the package with non-exported iterators, the method nextElem must be imported from iterators, and then the additional method unique to the package, exported, such that it is visible to the functions in the foreach package namespace. ...
written 22 months ago by ben.ward30
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custom iterators and foreach inside package - fails
... Hi, hopefully someone out there is good with foreach and iterators! I've been struggling with this:   I have created a custom iterator, inheriting from there iter class in the iterators package. The iterator and its methods are not exported from the package. Here is the iterator and a test functio ...
iterators foreach written 22 months ago by ben.ward30
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Comment: C: Using iterators and foreach with doMC, using DNAStringSets
... Thanks Dan! This looks like it might be exactly what I need. One question if anyone knows this - does the BiocPar methods or apply, mapply and so on work like I believe my own iterators do, in that they only send a subset of the data to a worker, to avoid the overhead of copying a large data object. ...
written 23 months ago by ben.ward30
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Exclude masked rownames in DNAMultipleAlignments
... Hi, why do sequence alignments with rowmasks still return the names of every row? Is there an easy way to get only the names of the sequences affected by the mask? e.g. origMAlign <- + readDNAMultipleAlignment(filepath = + system.file("extdata", + "msx2_mRNA.aln", + package="Biostrings"), ...
biostrings multiple sequences rownames masks rowmask written 23 months ago by ben.ward30 • updated 23 months ago by Valerie Obenchain ♦♦ 6.4k
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Using iterators and foreach with doMC, using DNAStringSets
... Hi, This is the first time I've programmed a parallel solution in R and Bioconductor, so I wanted to make a post and see if I've done this optimally/right! My problem was to do compute a series of sliding window based sequence identity scans between many pairs two sequences. To do this, I programme ...
parallel dnastringset iterators written 23 months ago by ben.ward30
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Comment: C: The way to window over sequences of a DNAStringSet
... Hi Herve, The sequences are aligned with gap characters, and so are the same length, and so the sub-sequences are taken from the same window on each original sequence. I use consensusMatrix to then calculate a few statistics like number of polymorphisms, allele frequencies, number of states per site ...
written 23 months ago by ben.ward30
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The way to window over sequences of a DNAStringSet
... Hi, if I have a DNAStringSet object, say 5 sequences, and I want to do a sliding window across those sequences and calculate `consensusMatrix` on only a some sites of the entire sequence, what is the best way to go about this? I think that for the selection of the sites I can use a mask, and I think ...
biostrings views mask window written 23 months ago by ben.ward30 • updated 23 months ago by Hervé Pagès ♦♦ 13k
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Counting SNPs where ambiguity codes represent heterozygosity.
... Hi, If I have two DNAStrings in a DNAStringSet, they are of the same length: > dna <- DNAStringSet(c("ATYGRTCGATCG", "MTSGATCRATCG")) > dna   A DNAStringSet instance of length 2     width seq [1]    12 ATYGRTCGATCG [2]    12 MTSGATCRATCG   How can I count the number of mismatches betwee ...
alignment biostrings snps written 2.4 years ago by ben.ward30 • updated 2.3 years ago by Hervé Pagès ♦♦ 13k
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Comment: C: Getting Aligned DNAStringSet from reference and BAM/SAM file(s)
... Thank you for explaining Herve, that does help a lot. I see so rather than an MSA, SAM is a whole lot of pairwise alignments with the reference. Therefore pursuing getting a FASTA "MSA" from SAM will result in loss of insertions. Will pileup ignore insertions to then since it returns info on a per b ...
written 2.8 years ago by ben.ward30

Latest awards to ben.ward

Scholar 22 months ago, created an answer that has been accepted. For A: custom iterators and foreach inside package - fails

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