ckmr2colony: make a rudimentary colony input file

In eriqande/CKMRsim: Inference of Pairwise Relationships Using Likelihood Ratios

make a rudimentary colony input file

Description

This takes a long format data frame of CKMR frequencies and a corresponding one of genotypes of individuals (gotta have LocIdx and alle1 and alle2 columns, which give the integer representation of the alleles). Then it spits out a colony file with allele freqs either specified (by default) or not.

Usage

ckmr2colony(
  CKF,
  CKG,
  freqs_known = TRUE,
  outfile = "Colony2.dat",
  err_rate = c(0.01),
  drop_rate = c(0.01)
)

Arguments

CKF	a data frame like long_markers that has the allele freqs and indexes, etc.
CKG	a data frame of genotype data. It needs to have these columns: id the identifier of the individual Locus the names of the loci LocIdx the index of the locus (should correspond exactly to CKF) alle1 The integer index of the allelic type of the first gene copy in the indiv. alle2 The integer index of the allelic type of the second gene copy in the indiv.
freqs_known	set to FALSE if you want Colony to estimate the allele freqs. Otherwise it will just use the freqs from CKF (This makes a lot of sense if you have 10,000 individuals but you don't want to run all of them in Colony)
outfile	path to the output file to send this to
err_rate	the per-locus rate of mis-genotyped loci assumed for the analysis. Recycles to the proper length.
drop_rate	the per-locus rate of assumed for the analysis. Recycles to the proper length.

Details

The idea is that you use this to follow up on clusters of pairs that look like they might be sibs of some sort. This spits out a Colony2.dat file that can be run with Colony. To change different settings and options for the run, you just hand edit that output file.

eriqande/CKMRsim documentation built on Aug. 2, 2024, 7:23 a.m.