analyze_MCMC: MCMC function for determing contamination probability and...
In eriqande/SNPcontam: Detecting contaminated samples from SNP genotypes
Description
Usage
Arguments
Value
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 16, 2019, 8:44 a.m.
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Description Usage Arguments Value
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.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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