partition_two_snppit_results: Partition the results of two SNPPIT runs by comparisons of...

In eriqande/HatcheryPedAgree:

Partition the results of two SNPPIT runs by comparisons of their features

Description

This function is intended to break down the results of two SNPPIT runs into non-overlapping groups of kids. The primary purpose for this is to compare runs with sex-and-date to runs without the sex and date. After doing this you can use a later function to pick out the trio from either run1 or run2 according to which category it is in.

Usage

partition_two_snppit_results(Run1, Run2, FDR1 = 0.01, FDR2 = 0.01)

Arguments

Run1	the output of slurp_snppit() for the first (typically with sex and date) snppit run.
Run2	the output of slurp_snppit() or reformat_no_sex_or_date_results() for the second (typically without sex and date) snppit run.
FDR1	the FDR threshold to consider for Run1 (defaults to 0.01).
FDR2	the FDR threshold to consider for Run2 (defaults to 0.01).

Details

This is implemented in terms of bit-masks. Here are the bits, given by the "1" value. We set this up so that good trios shared by both runs will be 0s.

• 1: Parents not identified (NA) in Run1

• 2: Parents not identified (NA) in Run2

• 4: Max posterior trio in Run1 is not C_Se_Se

• 8: Max posterior trio in Run2 is not C_Se_Se

• 16: FDR > FDR1 in Run1

• 32: FDR > FDR2 in Run2

• 64: Run1 and Run2 parent pairs share exactly 0 individuals

• 128: Run1 and Run2 parent pairs share exactly 1 individual

If neither of bits 1, 2, 64, or 128 are set, then there were two parents matching between the groups.

eriqande/HatcheryPedAgree documentation built on Sept. 21, 2023, 7:24 p.m.