User: aslanforever94

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Posts by aslanforever94

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How do you input a vcf snp file in R directly to run a PCA for the individuals?
... Hi, I have a raw vcf file composed of around 40,000 SNPs. I want to input it in R Studio and divide it into two files based on the SNP positions. I have done this and these two files currently exist as two independent unsaved data frames. After this I want to run a PCA and Fst analysis on these two ...
R snp written 3 months ago by aslanforever940
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What does NA imply in a plink.raw file for genotype calling?
... Hi, I used a filtered SNP vcf to run plink using the --recodeAD, --doubleid (my sample names have underscores) and --allow-extra-chr (the name of my chr was not being recognized). My plink.raw file has not only 0, 1, 2 but also many NAs in the samples, distributed randomly. I referred to the manual ...
snp written 3 months ago by aslanforever940 • updated 8 weeks ago by irlyn0

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