User: anailis

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anailis0
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Posts by anailis

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Comment: C: Incomplete GWAS Catalog Data from makeCurrentGwascat() [R, gwascat]
... Updated R so I could updated to this version and now it works :) Thanks! ...
written 12 days ago by anailis0
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Comment: C: Incomplete GWAS Catalog Data from makeCurrentGwascat() [R, gwascat]
... Thanks for the advice on variable naming, I've updated my post. I tried again this morning and can still only get the 6427 records. I wouldn't say that my internet is overly bad - it's not had problems downloading things before. Is your gwascat version the same as mine? ...
written 12 days ago by anailis0
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Incomplete GWAS Catalog Data from makeCurrentGwascat() [R, gwascat]
... I want to query GWAS Catalog using the `gwascat` package in R. I was surprised to see makeCurrentGwasCat() returns only 6,427 associations when there are many more in GWAS Catalog. Is this what I am meant to be observing, or is something going wrong here? > cat1 <- makeCurrentGwascat() ...
gwas catalog bioconductor gwascat R written 13 days ago by anailis0
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Comment: C: genomic inflation factor calculation
... @always_learning I think you have gotten confused: qchisq(0.5,1) is (approx) 0.456. You want to use: chisq <- qchisq(gwas$PVAL, 1, lower.tail = F) lambda <- median(chisq) / qchisq(0.5,1) OP's question cannot be answered without looking at their QQ plot, but I don't see ...
written 6 months ago by anailis0
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Comment: C: Q: Error converting vcf to hap
... Thank you for your response. I think I should have been working with GT. ...
written 7 months ago by anailis0
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Q: Error converting vcf to hap
... Hello. I am trying to convert a .vcf containing phased data to SHAPEIT .hap/.sample format using bcftools or Plink2. bcftools convert input.vcf --hapsample output.hap OR plink2 --vcf input.vcf --export haps --out output.hap PLINK gives the error "--exports haps cannot be used with missi ...
software error plink written 7 months ago by anailis0 • updated 7 months ago by chrchang5237.6k

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