User: Miss Agnieszka Aleksandra Golicz
- Reputation:
- 40
- Status:
- New User
- Location:
- Australia
- Last seen:
- 5 days, 7 hours ago
- Joined:
- 4 years, 7 months ago
- Email:
- a***************@uq.net.au
Posts by Miss Agnieszka Aleksandra Golicz
<prev
• 27 results •
page 1 of 3 •
next >
0
votes
1
answers
237
views
1
answers
... The non-parametric version just finished and the overlap is ~96%, so the answer most likely is the plots are good enough.
...
written 14 months ago by
Miss Agnieszka Aleksandra Golicz • 40
0
votes
1
answer
237
views
1
answer
... 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 14 months ago by
Miss Agnieszka Aleksandra Golicz • 40
0
votes
0
answers
473
views
0
answers
... 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 23 months ago by
Miss Agnieszka Aleksandra Golicz • 40
0
votes
1
answers
777
views
1
answers
... 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 3.5 years ago by
Miss Agnieszka Aleksandra Golicz • 40
0
votes
1
answers
777
views
1
answers
... I have share the file with you via cloudstore. You should have a link in your email box.
Best wishes,
Agnieszka
...
written 3.5 years ago by
Miss Agnieszka Aleksandra Golicz • 40
0
votes
1
answers
777
views
1
answers
... 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 3.5 years ago by
Miss Agnieszka Aleksandra Golicz • 40
0
votes
1
answer
777
views
1
answer
... 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 3.5 years ago by
Miss Agnieszka Aleksandra Golicz • 40
• updated 3.5 years ago by
Valerie Obenchain ♦♦ 6.7k
0
votes
1
answers
963
views
1
answers
... I can confirm that the code works on the full data set. Thanks for the fix!
Agnieszka
...
written 3.7 years ago by
Miss Agnieszka Aleksandra Golicz • 40
0
votes
1
answers
963
views
1
answers
... 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 3.7 years ago by
Miss Agnieszka Aleksandra Golicz • 40
0
votes
1
answers
963
views
1
answers
... 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 3.7 years ago by
Miss Agnieszka Aleksandra Golicz • 40
Latest awards to Miss Agnieszka Aleksandra Golicz
Popular Question
14 months ago,
created a question with more than 1,000 views.
For ggbio circular plot y axis scale
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.2.0
Traffic: 416 users visited in the last hour