runPedFac: Initialize pedigree run

In ngthomas/pedfac: Factor graph based pedigree sampler

Description

The function runPedFac prepares and runs a multigeneration pedigree sampler given input genetic data

Usage

runPedFac(geno.path, marker.path = "", output.path = "",
  random.seed = 26, n.iter = 1, cyclic.choice = 0,
  observe.frac = 0.8, max.unobs = 1, max.gen = 0, min.age = 1,
  max.age = 1, haplo.method = 0, geno.err = 0.02)

Arguments

geno.path	string. Path to the input genotype file (see checkGeno help for formatting). Required.
marker.path	string. Directed path to the option marker info file.
output.path	string. Path to store intermed and final output files. By default, outputPath will be set in an upper folder of the current user's working directory. Regarding sampling:
random.seed	postive integer. Random seed to pass on pedigree sampler. Default:26.
n.iter	positive integer. Number of sampling iteration. Default: 1.
cyclic.choice	integer from 0 to 2. Choices of handling loops or cyclic path in pedigree. Default: 0. 0 - not allowing loops; 1 - throttle method; 2 - decimation method
observe.frac	float value from 0 to 1. Assumed sampling fraction. Default: 0.8; use -1 for unknown.
max.unobs	nonnegative integer. Maximum number of unobserved individuals allowed in between any two individuals. Default: 1.
max.gen	nonnegative integer. Number of predecessor generation(s) considered beyond the earliest observed generation. Default: 0. Setting it as 0 means that individuals of the earliest observed generation are treated as founders. Regarding specie life history:
min.age	positive float value. Minimal age of sexual maturation or fecundity (in year). Default: 1.
max.age	positive float value. Maximum age of sexual maturation or fecundity (in year). Default: 1. Regarding genotype marker:
haplo.method	positive integer 0 - 2. Selected method in the case of handling multiallelic markers. Default: 0. 0 - taking the most informative allele whose frequency is closest to 0.5; 1 - (not avail) deconstructing haplotype into a set of nucleotide units; 2 - (not avail) reduce the multiallelic basis into n class of binomial switches
geno.err	float value from 0 to 1. Assumed background genotype error rate in the form of epsilon. Default: 0.02. If the genotype error row - 'gerror' of marker_info.txt is provided, this param will be overridden.

Examples

# runHaplot(run.label, sam.path, label.path, vcf.path)
runPedFac(geno.path="/Users/thomasn/repo/pedfac/example/case_0/genotype.txt")

ngthomas/pedfac documentation built on Dec. 10, 2020, 6:28 p.m.