User: Lna

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Lna0
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Posts by Lna

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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 4 months 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 4 months ago by Lna0 • updated 4 months ago by Valerie Obenchain ♦♦ 6.4k
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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 5 months 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 5 months ago by Lna0 • updated 5 months ago by Valerie Obenchain ♦♦ 6.4k
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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 5 months 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 5 months ago by Lna0 • updated 5 months ago by Stephanie M. Gogarten530
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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 9 months 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 9 months ago by Lna0
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Answer: A: "set genotype" function for gds?
... Thank you! That worked fine! ...
written 9 months 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 9 months ago by Lna0

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