## User: ben.ward

ben.ward30
Reputation:
30
Status:
New User
Location:
United Kingdom
Last seen:
3 years, 6 months ago
Joined:
4 years, 9 months ago
Email:
b*******@sainsbury-laboratory.ac.uk

#### Posts by ben.ward

<prev • 14 results • page 1 of 2 • next >
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... 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){ ...
written 3.7 years ago by ben.ward30 • updated 3.7 years ago by Martin Morgan ♦♦ 23k
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... 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 3.7 years ago by ben.ward30
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... 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 ...
written 3.7 years ago by ben.ward30
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... 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 3.8 years ago by ben.ward30
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... 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"), ...
written 3.8 years ago by ben.ward30 • updated 3.8 years ago by Valerie Obenchain6.7k
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... 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 ...
written 3.8 years ago by ben.ward30
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... 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 3.8 years ago by ben.ward30
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... 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 ...
written 3.8 years ago by ben.ward30 • updated 3.8 years ago by Hervé Pagès ♦♦ 14k
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... 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 ...
written 4.2 years ago by ben.ward30 • updated 4.2 years ago by Hervé Pagès ♦♦ 14k
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... 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 4.6 years ago by ben.ward30

#### Latest awards to ben.ward

Scholar 3.7 years ago, created an answer that has been accepted. For A: custom iterators and foreach inside package - fails

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