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Questions tagged [plink-genomics]

Plink is a whole genome association analysis toolset developed by Shaun Purcell. Use this tag to describe questions regarding the plink api, or operations on plink file types (.map, .ped, .fam, .bed etc) Do not use this tag for questions regarding the PuTTY command-line connection tool Plink

Plink is a whole genome association analysis toolset developed by Shaun Purcell while at the Center for Human Genetic Research at MGH. This toolset is a bioinformatics tool used to perform analysis of genotype/phenotype data.

Do not confuse this with PuTTY Plink, the command-line connection tool.

Documentation for the tool and its datasets can be found on the Official Website for Plink

Questions regarding the toolset can also be found on Biostars and on the Bioinformatics Stack Exchange.

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How to determine LOD threshold for significant QTL for analysis?

` #Permutation test operm10 <- scanone(boltbdh23_SPAD,method = "em",n.perm=1000,verbose = TRUE) summary(operm10) > summary(operm10) LOD thresholds (1000 permutations) lod 5% 3.05 10% 2.69 #Looking for qtls #scanone em…
Abhijeet Chauhan
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How to replace a column in .fam with .txt in unix

I am looking for some options in unix (may be awk or sed ) through which I can replace the last column in my .fam file with the last column (v8) of a .txt file. Something similar to the merge function in R. My .fam file looks like this 20481 20481 0…
Aryh
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