User: Lna

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Lna0
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Posts by Lna

<prev • 30 results • page 1 of 3 • next >
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Comment: C: SNPs in multiple locations
... Thank you very much for the detailed explanation. Sorry, I forgot to add the annotation source, yes, I also used TxDb.Hsapiens.UCSC.hg19.knownGene. Now I understand how the output is generated based on the annotation package, but I still don't really understand how to relate it to the information ...
written 2.1 years ago by Lna0
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SNPs in multiple locations
... Dear all, I used the locateVariants() function in the VariantAnnotation package to annotate a big list of SNPs and I'm having some problems interpreting the results. I checked for all available locations (intergenic, intron, coding, fiveUTR, threeUTR, promoter and splicesite) and I found out that ...
variantannotation annotation locatevariants ucsc txdb.hsapiens.ucsc.hg19.knowngene written 2.1 years ago by Lna0 • updated 2.1 years ago by Valerie Obenchain6.7k
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Comment: C: No annotation for single SNPs
... Thank you for your answer, but honestly... now I am totally confused. I am using the AllVariants() parameter, because I thought this would provide me all types of available annotation, including the output of CodingVariants(), IntronVariants(), FiveUTRVariants(), ThreeUTRVariants and so on. (I thoug ...
written 2.2 years ago by Lna0
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No annotation for single SNPs
... Dear all, I want to annotate all SNPs on my Illumina Chip. I generated a vcf file containing all 4284426 SNPs with: loc <- locateVariants(target, TxDb.Hsapiens.UCSC.hg19.knownGene, AllVariants(promoter=PromoterVariants(downstream=500))) I do not get a result for every entry in my vcf file. Wh ...
variantannotation snps ucsc txdb.hsapiens.ucsc.hg19.knowngene written 2.2 years ago by Lna0 • updated 2.2 years ago by Valerie Obenchain6.7k
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Comment: C: Error using readVcf
... Thank you for your answer. When I first used VariantAnnotation the alleleA/alleleB columns were not included in the SNP annotation, so I had no problem with that... In the meanwhile I added the columns from the Illumina table with the SNP information and they include "N","D" and "I" apart from the s ...
written 2.2 years ago by Lna0
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Error using readVcf
... Dear all, I'm trying to obtain annotations for SNPs I analysed in GWASTools. Some time ago it worked fine by using the line vcfWrite(genoData,vcf.file=vcf.file,id.col="snpID",snp.exclude=snp.excl) to write the vcf file from the data objects in GWASTools and reading the vcf file with vcf <- re ...
variantannotation gwastools written 2.2 years ago by Lna0 • updated 2.2 years ago by Stephanie M. Gogarten670
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Comment: C: "set genotype" function for gds?
... Thank you! Now everything seems to work. Maybe it would make sense to include this information in the help text for write.gdsn... ...
written 2.5 years ago by Lna0
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Comment: C: "set genotype" function for gds?
... There's one thing... When I read an entry for one SNP which includes "NA"s  (like: NA   NA   NA   NA   NA   NA   NA   NA    2    NA    NA    NA    NA    NA    NA    NA     1    NA    NA    NA     2    NA     2   2  NA    NA    NA    NA) from a gds file and try to write it with write.gdsn to anothe ...
written 2.5 years ago by Lna0
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Answer: A: "set genotype" function for gds?
... Thank you! That worked fine! ...
written 2.5 years ago by Lna0
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"set genotype" function for gds?
... I'm using GWASTools for my GWAS analysis. It turned out that there are some genotyping problems with a few hundred SNPs on the X-chromosome. I already have all my data stored in gds files for use in GWASTools and I want to change the genotypes of the erroneous SNPs directly in the gds file. I was ho ...
gwastools gds written 2.5 years ago by Lna0

Latest awards to Lna

Popular Question 2.1 years ago, created a question with more than 1,000 views. For Use of org.Hs.eg.db and TxDb.Hsapiens.UCSC.hg19.knownGene
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Upgrade to Bioconductor 3.4 - problems with R
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Upgrade to Bioconductor 3.4 - problems with R

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