User: Richard Pearson
Richard Pearson • 60
- Reputation:
- 60
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- New User
- Location:
- Last seen:
- 6 years, 3 months ago
- Joined:
- 7 years, 2 months ago
- Email:
- 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 Pearson • 60
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... 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, ...
written 6.3 years ago by
Richard Pearson • 60
• updated
6.3 years ago by
Valerie Obenchain • 6.7k
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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 Pearson • 60
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... 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 Pearson • 60
• updated
6.6 years ago by
Michael Lawrence ♦ 11k
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... 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"]] ...
written 6.9 years ago by
Richard Pearson • 60
• updated
6.9 years ago by
Valerie Obenchain • 6.7k
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... 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 Pearson • 60
• updated
7.2 years ago by
Valerie Obenchain • 6.7k
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