calc_EM: Function to use EM algorithm to estimate the genotype...
In Struglab/RVS: Robust Variance Score (RVS) test for association of variants from next generation sequence data with binary traits using external controls
Description
Usage
Arguments
Value
Description
Given a matrix (M) with dimension number of sample by 3 consisting of genotype likelihoods for each individual, this function uses the EM algorithm to estimate genotype frequencies.
It returns a vector with three decimals to stands for probability of 0, 1 or 2 minor alleles in the whole sample
Usage
1
calc_EM(M)
Arguments
M
matrix of genotype likelihoods derived from Phred-scale likelihood in VCF input for one variant.
Value
a vector with three decimals to stands for probability of 0, 1 or 2 minor alleles.
Struglab/RVS documentation built on May 9, 2019, 3:11 p.m.
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.
Description Usage Arguments Value
Description
Given a matrix (M) with dimension number of sample by 3 consisting of genotype likelihoods for each individual, this function uses the EM algorithm to estimate genotype frequencies. It returns a vector with three decimals to stands for probability of 0, 1 or 2 minor alleles in the whole sample
Usage
1 | calc_EM(M)
|
Arguments
M |
matrix of genotype likelihoods derived from Phred-scale likelihood in VCF input for one variant. |
Value
a vector with three decimals to stands for probability of 0, 1 or 2 minor alleles.
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.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.