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filipluca / Polygenic_SA_selection_in_the_UK_Biobank

Polygenic signals of sex differences in selection in humans from the UK Biobank
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filtered individuals file #1

Open humanpaingeneticslab opened 11 months ago

humanpaingeneticslab commented 11 months ago

Hi,

In step 2 there's usage of a file: plink2 ... --keep ~/Documents/biobank/ukb_phenotypes/indiv_filtered_v2.txt

However, the closest thing I can see for that file is at step 3 where the file is written: write.table( bd6[,c(1,1)], "ukb_phenotypes_v3/indiv_filtered_v2.txt"

-> same file name but different folders: (ukb_phenotypes vs ukb_phenotypes_v3) Q. are they supposed to be the same file? -> Q. should step 3 be done before step 2?

Any help appreciated!

filipluca commented 11 months ago

Hi,

You're right that step 3 (filtering phenotypes) needs to be done before step 2 (filtering sites). There must be a good reason why I ordered it as such, but I can't recall just now.

And I renamed all the folders with the suffix "_v3" to denote that they 'final' versions. In the case of the phenotype folder, there were no file changes from initial folder name to v3, so the content of /ukb_phenotypes is the same as /ukb_phenotypes_v3, despite the name change.

Filip

PS: Haven't replied to your email yet. I should be less busy the week after next, so happy to chat then. Otherwise just post issues here and I'll reply when I can.