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 11 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 11 months ago by Lna0 • updated 11 months ago by Valerie Obenchain ♦♦ 6.5k
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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 12 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 12 months ago by Lna0 • updated 12 months ago by Valerie Obenchain ♦♦ 6.5k
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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 12 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 12 months ago by Lna0 • updated 12 months ago by Stephanie M. Gogarten560
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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 16 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 16 months ago by Lna0
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Answer: A: "set genotype" function for gds?
... Thank you! That worked fine! ...
written 16 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 16 months ago by Lna0

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