Description Usage Arguments Value Author(s) References Examples
Genotype-call tool for single-sample next generation sequencing data using empirical Bayes method.
1 | ebSNP(dat, T1 = 0.5, T2 = 0.5, eps = 0.001, maxstep = 30)
|
dat |
A data matrix with two rows, containing the number of major and minor alleles at each position. Each column corresponds to one position. |
T1 |
Lower threshold for genotyping. |
T2 |
Upper threshold for genotyping. |
eps |
Stopping criteria of EM algorithm. |
maxstep |
Maximum number of EM iterations. |
A list,
pi0.hat |
Estimate for pi0, the probability of a position bearing a homozygous genotype. |
alpha.hat |
Estimate for alpha. |
beta.hat |
Estimate for beta. |
delta |
1-g_i. |
G |
Estimated genotypes. |
Na You
Single-sample SNP Detection By Empirical Bayes Method Using Next Generation Sequencing Data
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