sequoiaSim: Estimate error expected with your baseline using Sequoia for...

In delomast/singleSequoia: Tools for Single Parent Assignment with Sequoia

Estimate error expected with your baseline using Sequoia for single parent assignment

Description

sequoiaSim runs simulations to estimate the error expected when using sequoia for single parent assignments with your baseline

Usage

sequoiaSim(
  input_parameters,
  LLR_min = 0.5,
  parent_data_file,
  min_genotyped = 0.9,
  allele_error_rate = 0.001,
  Seq_MaxMismatch = NA,
  prefix = ""
)

Arguments

input_parameters	This is a dataframe of input parameters to control the simulations. For example: parameters <- data.frame(Proportion_baseline_sampled = c(1, .9, .85, .75), Number_of_simulations_to_run = c(100, 200, 200, 200), Number_of_offspring = c(1000, 3000, 3000, 3000), Parent_expansion = c(TRUE, TRUE, TRUE, TRUE) )
LLR_min	This is the minimum LLR you want to use to accept a single parent assignment
parent_data_file	This is either a dataframe or a file path to a csv with a header and your baseline data in it. Each row is an individual, and columns are: PopulationName,IndividualName,Sex,SNP1,SNP2,SNP3,... Sex is either M or F, SNPs are one call per column and one character per allele (ie, AT, TT, AA) Individual names must be unique, even across populations. This file can be generated using the toSequoiaSimulation function.
min_genotyped	This is the proportion of genotypes that must be non-missing (ie 0.9 for 90% of genotypes) to include a simulated parent or offspring in the analysis
allele_error_rate	This is the per allele genotyping error rate
Seq_MaxMismatch	This is the MaxMismatch parameter to use for Sequoia. If not specified, the default is to use 5% of the number of markers in your panel (rounded up to the nearest integer).
prefix	This is the prefix to add to the output file name. Default is no prefix.

Details

This runs simulations given the parameters you input, see the separate writeup for a full description of how the simulations are run.

Value

This function writes its output as a csv to the working directory afeter all simulations have finished.

delomast/singleSequoia documentation built on June 14, 2022, 1:08 p.m.