User: Miss Agnieszka Aleksandra Golicz

Reputation:
40
Status:
New User
Location:
Australia
Last seen:
4 months, 2 weeks ago
Joined:
5 years, 5 months ago
Email:
a***************@uq.net.au

Posts by Miss Agnieszka Aleksandra Golicz

<prev • 29 results • page 1 of 3 • next >
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regioneR meanInRegions to evaluate mutation accumulation
... Hi, The regioneR manual says: meanInRegions The meanInRegions function is useful when we want to evaluate the relation of a RS against some sort of numeric value. For example, we could test whether the methylation levels of our RS is higher than expected, or if it accumulates fewer mutation than ...
regioner written 5 months ago by Miss Agnieszka Aleksandra Golicz40 • updated 5 months ago by bernatgel120
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Is localZScore function of regioneR mask-aware?
... Hi, I was wondering if the localZScore function of regioneR is mask-aware? Does it skip the masked regions? if not, is it possible to make it mask-aware? All the best, Agnieszka ...
regioner written 5 months ago by Miss Agnieszka Aleksandra Golicz40 • updated 5 months ago by bernatgel120
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Answer: A: Combat prior plots good enough?
... The non-parametric version just finished and the overlap is ~96%, so the answer most likely is the plots are good enough.  ...
written 2.0 years ago by Miss Agnieszka Aleksandra Golicz40
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Combat prior plots good enough?
... 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 ...
combat combat sva written 2.0 years ago by Miss Agnieszka Aleksandra Golicz40
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OmicCircos barplot height and scale
... 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 ...
omiccircos written 2.8 years ago by Miss Agnieszka Aleksandra Golicz40
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Comment: C: readVcf shape of 'skeleton' is not compatible with 'NROW(flesh)'
... 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 4.3 years ago by Miss Agnieszka Aleksandra Golicz40
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Comment: C: readVcf shape of 'skeleton' is not compatible with 'NROW(flesh)'
... I have share the file with you via cloudstore. You should have a link in your email box. Best wishes, Agnieszka ...
written 4.3 years ago by Miss Agnieszka Aleksandra Golicz40
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Comment: C: readVcf shape of 'skeleton' is not compatible with 'NROW(flesh)'
... 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 4.3 years ago by Miss Agnieszka Aleksandra Golicz40
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readVcf shape of 'skeleton' is not compatible with 'NROW(flesh)'
... 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 ...
variantannotation written 4.3 years ago by Miss Agnieszka Aleksandra Golicz40 • updated 4.3 years ago by Valerie Obenchain6.7k
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Comment: C: predictCoding error DNAStringSet_translate
... I can confirm that the code works on the full data set. Thanks for the fix! Agnieszka ...
written 4.6 years ago by Miss Agnieszka Aleksandra Golicz40

Latest awards to Miss Agnieszka Aleksandra Golicz

Popular Question 10 months ago, created a question with more than 1,000 views. For predictCoding error DNAStringSet_translate
Popular Question 10 months ago, created a question with more than 1,000 views. For makeTranscriptDbFromGFF Unexpected transcript duplicates
Popular Question 2.0 years ago, created a question with more than 1,000 views. For ggbio circular plot y axis scale

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