analyze_MCMC: MCMC function for determing contamination probability and...

Description Usage Arguments Value

View source: R/analyze_MCMC.R

Description

Description

Usage

1
analyze_MCMC(MCMC, burnin = 100)

Arguments

MCMC

A list that contains the outputs of the contam_MCMC function, including the rho output, the allele frequency output, and the z value output from all sweeps.

burnin

The number of sweeps at the beginning of the MCMC that will be disregarded for analysis.

Value

Returns a list of three named components:

allele_pm

A vector containing the posterior mean of the allele frequencies for each allele.

rho_pm

One value, which is the poterior mean of the contamination proportion.

z_pm

A vector containing the posterior mean of the z value for each individual. A z_pm value 1 at the ith index would indicate that the ith individual was indentified as contaminated in each sweep.


eriqande/SNPcontam documentation built on May 13, 2017, 8:20 p.m.