Plink input, phenotypes and multiple testing

Question

[John E]

I have final reports from Illumina beadchips. The reports only include Allele 1 TOP and Allele 2 TOP. Making input files for Plink (.map .lgen .fam), is it required to convert Top to Forward? If required, do you have a suggestion on how to do so?

Is it possible to provide Plink with multiple phenotype parameters at once? Could for example a matrix be loaded (subjects and phenotypes), so that Plink will automatically analyze such and correct for multiple testing? Or can Plink only be given one phenotype parameter to analyze at any given moment. Does any other software give the opportunity to analyze multiple phenotype parameters?

Thanks a lot!

Answer 1

[chrchang523]

Plink can process multiple phenotypes in one run: see the --all-pheno flag (more discussion at http://pngu.mgh.harvard.edu/~purcell/plink/anal.shtml). However, its multiple testing corrections only account for multiple variants, not multiple phenotypes.