Bugfix: manhattan.R now indexes with BP, not SNP which should be an optional column #72
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As the title suggests, the manhattan function does not require a SNP column, but when creating the index (to handle the cases where there are missing chromosomes), it uses the CHR and (possibly non-existent) SNP column. I have replaced the call to
d$SNPwithd$BP, which is a required column and produces the same result as usingd$SNP(when it exists).I'm honestly not sure how this has been broken for 7 years without a fix...