User: Miss Agnieszka Aleksandra Golicz
- Reputation:
- 40
- Status:
- New User
- Location:
- Australia
- Last seen:
- 4 months, 2 weeks ago
- Joined:
- 4 years, 11 months ago
- Email:
- a***************@uq.net.au
Posts by Miss Agnieszka Aleksandra Golicz
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... The non-parametric version just finished and the overlap is ~96%, so the answer most likely is the plots are good enough.
...
written 18 months ago by
Miss Agnieszka Aleksandra Golicz • 40
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... Hi,
I read that the plots have to be really bad to cause a difference between parametric and non-parametric results, but I could not find any plots for comparison. Do you think with my plots I can still get away with using parametric ComBat?
The url for plots: https://ibb.co/mMwMQb
Any help would ...
written 18 months ago by
Miss Agnieszka Aleksandra Golicz • 40
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... Hi,
I'm trying to use OmicCircos to plot log(FPKM) as a barplot. It seems to be working fine, other than the barplot seems to have a default height even if the the value of expression is 0. This can be seen when I add scale. 0 on the scale corresponds to an already sizable bar. This gives a false ...
written 2.3 years ago by
Miss Agnieszka Aleksandra Golicz • 40
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... Hi Valerie,
After consulting this thread: https://support.bioconductor.org/p/67946/#68122
I have added FORMAT fields into the header.
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DP,Number=1,Type=String,Description="Read Depth">
But readVcf() did not work ...
written 3.8 years ago by
Miss Agnieszka Aleksandra Golicz • 40
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... I have share the file with you via cloudstore. You should have a link in your email box.
Best wishes,
Agnieszka
...
written 3.8 years ago by
Miss Agnieszka Aleksandra Golicz • 40
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... Hi,
I have used scanVcf() and it seems to have worked:
> scn <- scanVcf(tab, param=param)
> names(scn[[1]])
[1] "rowRanges" "REF" "ALT" "QUAL" "FILTER" "INFO"
[7] "GENO"
> lapply(scn[[1]], length)
$rowRanges
[1] 413361
$REF
[1] 413361
$ALT
[1] 413361
$QUAL
[1] 4 ...
written 3.8 years ago by
Miss Agnieszka Aleksandra Golicz • 40
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... Hello,
I have a piece of code that have worked on three vcf files but failed on fourth. For the files the reference, samples and gff3 files are the same, only SNP calling algorithm is different.
The error I'm getting is:
Error in relist(v, part) :
shape of 'skeleton' is not compatible with 'NRO ...
written 3.8 years ago by
Miss Agnieszka Aleksandra Golicz • 40
• updated
3.8 years ago by
Valerie Obenchain • 6.7k
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... I can confirm that the code works on the full data set. Thanks for the fix!
Agnieszka
...
written 4.1 years ago by
Miss Agnieszka Aleksandra Golicz • 40
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... Thanks again. I understand that the fixes are in the devel version of VariantAnnotation. I will have to wait for my admin to install R-devel and will try it out.
...
written 4.1 years ago by
Miss Agnieszka Aleksandra Golicz • 40
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... For the future could you tell me how to remove problematic lines.
I tried:
invalid <- c(123)
vcf2 <- vcf[!invalid], but this did not seem to work.
Agnieszka
...
written 4.1 years ago by
Miss Agnieszka Aleksandra Golicz • 40
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For ggbio circular plot y axis scale
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