Tag: .fam

Plink Alternative Phenotype File Columns not being Read

Plink Alternative Phenotype File Columns not being Read 0 Hi, I have a plink alternative phenotype file with the following format: FID IID Phenotype 1 2 1 1 3 0 etc. As outlined in the plink documentation. zzz.bwh.harvard.edu/plink/data.shtml#pheno However, when I run the following command : plink –bfile ../Plink_Files/plink –logistic…

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SNP extraction

SNP extraction 0 I want to extract specific SNPs of interest i have in a text file into an additive genetics model so that each SNP can be in a 0/1/2 format for each subject using genetics info in from PLINK (.bed, .bim, and .fam files). How can i do…

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Question about ROH analysis by Plink 1.9

Hi all, I have recently tried to estimate runs of homozygosity (ROH) from my vcf file by using plink 1.9. I ran following code to generate binary files that plink required: plink –vcf myfile.vcf –make-bed –out out_name –no-sex –no-parents –no-fid –no-pheno –allow-extra-chr This vcf file only contains one individual and…

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Phenotype file for eQTL analysis using GEMMA

Phenotype file for eQTL analysis using GEMMA 0 Hello All, I appreciate it if someone could direct me in this regard. I am running eQTL analysis using GEMMA software. I have corrected the expression file with all samples (280 samples) and the genotype file is (170). I have a couple…

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What does .bim .bed .fam stands for?

What does .bim .bed .fam stands for? 1 I have a hard time differentiating these files, maybe understanding the acronyms could help. If I’m right .ped is from pedigree and .bed is a strange way to say ‘binary-pedigree’. The others are obscure. plink fam bim bed • 21 views •…

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