User: yduan004

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yduan00420
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Riverside
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4 months ago
Joined:
5 months, 2 weeks ago
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y*******@ucr.edu

Posts by yduan004

<prev • 8 results • page 1 of 1 • next >
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Comment: C: SNP location annotation problem in "VariantAnnotation" package
... Ok, I see. Thanks for your answering! Yuzhu ...
written 5 months ago by yduan00420
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Comment: C: SNP location annotation problem in "VariantAnnotation" package
... I think if the snps don't fall within transcripts, then the location annotation should be intergenic, intron or somewhere else. But in this case, all of the locations are NA... What do you think about it? Thanks! ...
written 5 months ago by yduan00420
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Comment: C: SNP location annotation problem in "VariantAnnotation" package
... Hi Nanda, Sorry about that. I have now figured out how to make the links publicly accessible. Could you please check it again? Thanks! Yuzhu ...
written 5 months ago by yduan00420
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Comment: C: Error when running "locateVariants" function in "VariantAnnotation" package
... Hi Martin, Thanks for identifying the problem! I hope this bug can be fixed in the next release of R! Cheers, Yuzhu ...
written 5 months ago by yduan00420
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Comment: C: Error when running "locateVariants" function in "VariantAnnotation" package
... Hi Herve,  Thanks for your solution! I am looking forward to using your new release of S4Vectors package! Cheers, Yuzhu ...
written 5 months ago by yduan00420
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Comment: C: Error when running "locateVariants" function in "VariantAnnotation" package
... Hi Nanda, thanks for answering my question. I ran this trunk of code ## Start a new R session library(tidyverse) library(GenomicFeatures) library(VariantAnnotation) rd_test <- readRDS("rd_test.rds") txdb <- loadDb("Homo_sapiens.GRCh38.90.sqlite") allvar <- locateVariants(rd_test, txdb, A ...
written 5 months ago by yduan00420
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Error when running "locateVariants" function in "VariantAnnotation" package
... I met an error when running "locateVariants" function in "VariantAnnotation" package. Before running "locateVariants" function, I need to first libarary "tidyverse", but when I library "tidyverse" package before "VariantAnnotation" and run "locateVariants" function, an error happens ("Error in as.ve ...
variantannotation genomicfeatures tidyverse written 5 months ago by yduan00420 • updated 5 months ago by Hervé Pagès ♦♦ 13k
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SNP location annotation problem in "VariantAnnotation" package
... I couldn't get location annotation for some SNPs by using "VariantAnnotation" package. For some SNP ids, eventhough their GRanges data are normal as others, they couldn't be annotated by using "locateVariants" function. Here is the code I ran. The link for "abnorm_snpid.txt" is https://drive.google ...
variantannotation annotation written 5 months ago by yduan00420 • updated 5 months ago by Valerie Obenchain ♦♦ 6.4k

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