User: Richard Pearson

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Last seen:
6 years, 3 months ago
Joined:
7 years, 2 months ago
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r*******@well.ox.ac.uk

Posts by Richard Pearson

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Comment: C: writeVcf bug
... Hi Valerie That's great, thanks. Will check out the new code when available. Sorry, I worded this poorly. I simply meant that the problem I had previously seen with the example code ("Error in row(genoMat)") had gone away, but I had noticed a new problem with this same code. There are no other pro ...
written 6.3 years ago by Richard Pearson60
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writeVcf bug
... Hi I've recently upgraded to R 3.0.0, but am still having a (now slightly different) problem with writeVcf. When there is only one element in geno(vcf), each variant gets a separate row for each sample. For example, in the following code, out1.vcf has 5 variants, each with genotypes for 3 samples, ...
variantannotation written 6.3 years ago by Richard Pearson60 • updated 6.3 years ago by Valerie Obenchain6.7k
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Comment: C: writeVcf bug
... Hi Michael My devel sessionInfo is below. It seems biocLite has given me version 1.5.17of the package, but I see that .makeVcfGenolooks different in the latest from SVN (1.5.19) - so I'm sure you're right and I just need to wait for things to filter through. Apologies for the noise. Every time I u ...
written 6.6 years ago by Richard Pearson60
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writeVcf bug
... Hi I've noticed a bug with writeVcf when trying to write out relatively simple vcf files, e.g. a file containing only GT in the FORMAT fields. The following is a (hopefully) reproducible example based on examples in ?writeVcf library(VariantAnnotation) fl <- system.file("extdata", "ex2.vcf", pa ...
written 6.6 years ago by Richard Pearson60 • updated 6.6 years ago by Michael Lawrence11k
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Subsetting "sites only" VCF objects
... Hi It is wonderful that we can create subsets of VariantAnnotation VCF objects using [ but I have found that this doesn't work for VCFs that are "sites only", i.e. have no information in geno(vcf): > geno(vcf) SimpleList of length 0 > passVcf <- vcf[values(fixed(vcf))[["FILTER"]] ...
variantannotation written 6.9 years ago by Richard Pearson60 • updated 6.9 years ago by Valerie Obenchain6.7k
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Subset of samples with VariantAnnotation::readVcf
... Hi Is it possible to read in data on a subset of samples with readVcf? The only way I've found of doing this is to read in data on all samples, then subset, but it would be much more efficient for me to read in data only for my samples of interest. Apologies if I've missed something obvious. Rich ...
written 7.2 years ago by Richard Pearson60 • updated 7.2 years ago by Valerie Obenchain6.7k

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