Description Usage Arguments Details Value Author(s) See Also
Provides estimates of admixture proportions in offspring and ungenotyped parents, using phased data
1 | LEAPFrOG_EM(data,p,chr,alpha=1e-6)
|
data |
2 column matrix of allele counts, with each row as a SNP. Columns 1 and 2 refer to the 2 haplotypes. Each entry is either 1, 0 or NA. |
p |
Matrix of allele frequencies. Each row corresponds with a SNP. Number of rows must equal length of data. Each column is a population |
chr |
Vector of chromosome identifiers, one for each SNP. Each entry is an integer, 1-22 for the autosomes. If two X chromosomes for a female are being analysed, it should be identified by the number 23. |
alpha |
Convergence tolerance for the EM algorithm. The optimisation will stop when an interation fails to change the parental admixture proportions (total change across all parameters) by this amount |
LEAPFrOG_EM requires python to be installed. Only the parental admixture proportions are estimated directly (all except the last population), and therefore standard errors are only reported for these only.
A list including elements
m |
A vector: Admixture proportions (one per population) for the genotyped offspring. |
P1 |
A vector: Admixture proportions (one per population) for parent 'A'. |
P2 |
A vector: Admixture proportions (one per population) for parent 'B'. |
P1se |
A vector: Standard errors (All populations except the last) foradmixture proportions in parent 'A'. |
P2se |
A vector: Standard errors (All populations except the last) foradmixture proportions in parent 'A'. |
iterations |
Number of expectation steps performed. |
value |
Value of the likelihood function for the final maximisation step. |
Daniel Crouch & Michael Weale, Department of Medical and Molecular Genetics, King's College London
LEAPFrOG
,LEAPFrOG_plot
,BEAPFrOG
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