Are flags like --maf, --min-mac, --geno, and --mind testing > or >= ?

[Kristen]

Hello,

I am trying to document some details of QC for a dataset, and I want to make sure I am correct in when I use > and < vs. using >= and <=.

Can you please help me find out whether the following Plink flags are using strict inequality or are using >= or <= ? (In other words, whether something exactly equal to the threshold specified will be kept or excluded by each flag.)

--maf

--max-maf

--mac

--max-mac

--geno

--mind

--hwe

I think --maf 0.01 might keep variants with MAF==0.01, based on the documentation stating that it "filters out all variants with allele frequency below the provided threshold", and I would guess --mac probably works similarly.

I'm not sure about the upper bound allele frequency flags, --max-mac/--max-maf.

For --geno 0.05 and --mind 0.05 I suspect they may keep samples/variants where the missingness is exactly 0.05, based on the documentation stating that "--geno filters out all variants with missing call rates exceeding the provided value (default 0.1) to be removed, while --mind does the same for samples."

For --hwe, the documentation states that it "filters out all variants which have Hardy-Weinberg equilibrium exact test p-value below..." so my guess would be that it keeps variants where the HWE p-value is exactly equal to the threshold.

Can you please help me confirm the expected behavior of each of these flags when a variant or person has a value exactly equal to the specified threshold?

Is there a general "rule of thumb" for everything in Plink regarding whether flags specifying a threshold apply strict or non-strict inequality, or will this vary by flag?

Thank you,

Kristen

[Chris Chang]

The rule is that exact ties are not filtered out by any of these flags.

--
You received this message because you are subscribed to the Google Groups "plink2-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to plink2-users...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/plink2-users/e1635b55-5584-4605-bac5-796d045e4ecbn%40googlegroups.com.