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Meta analysis on 2 genotyping data set

Hi Please is there any tutorial or help on.doing meta anlysis in R on genotyping data sets ( about 300 000) SNP , three case control studies all genotype with same DNA chip, my questions are : 1/which r package do you advise me ? 2/ can you help with a detailed tutorial with different steps : data preparation tests ... 3/ is it possible to do a meta analysis on gwas data with an interaction term ? If yes how ? Thank you very much, any help is welcomed :)

snp r
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written by mel22 mel22

2 answers

Not sure for R, but a lot of people use METAL to perform meta analysis. You can refer to their manual here

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written by Sam Sam

Thank you very much Sam

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written by mel22 mel22

It seems that to use METAL i need to have separately a file for each marker : - Is there a bash code that i can use to extract a file for each marker from a big one file ? -Is there any alternative to METAL to do this with R ( I am more used to R :( ...)

THANK YOU VERY MUCH

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written by mel22 mel22

Think you only need the summary statistic files. You can follow their quick start page which provide the examples and scripts

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written by Sam Sam

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