MLEL: Max Likelihood Estimation of Linkage
In jendelman/MapRtools: Tools for genetic mapping
MLEL R Documentation
Max Likelihood Estimation of Linkage
Description
Max Likelihood Estimation of Linkage
Usage
MLEL(geno, pop.type, LOD, n.core = 1, adjacent = FALSE)
Arguments
geno
Matrix of haplotype dosages (markers x indiv)
pop.type
One of the following: "DH","BC","F2","S1","RIL.self","RIL.sib"
LOD
Logical, whether to return LOD (TRUE) or recomb freq (FALSE)
n.core
For parallel execution on multiple cores
adjacent
Logical, should calculation be done for all pairs (FALSE) or adjacent (TRUE) markers
Details
Can be used to estimate either the LOD score or recombination frequency, depending on the value of LOD. Genotype coding must represent dosage of a founder haplotype. For BC populations, possible allele dosages are 0,1. For DH and RIL pops, it is 0,2. For F2 and S1 pops, it is 0,1,2.
Value
If adjacent is FALSE, a matrix of recombination frequencies or LOD scores; otherwise, a three-column data frame with marker, the LOD or r value, and the phase ("c","r") with the previous marker
jendelman/MapRtools documentation built on April 12, 2025, 12:46 p.m.
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| MLEL | R Documentation |
Max Likelihood Estimation of Linkage
Description
Max Likelihood Estimation of Linkage
Usage
MLEL(geno, pop.type, LOD, n.core = 1, adjacent = FALSE)
Arguments
geno |
Matrix of haplotype dosages (markers x indiv) |
pop.type |
One of the following: "DH","BC","F2","S1","RIL.self","RIL.sib" |
LOD |
Logical, whether to return LOD (TRUE) or recomb freq (FALSE) |
n.core |
For parallel execution on multiple cores |
adjacent |
Logical, should calculation be done for all pairs (FALSE) or adjacent (TRUE) markers |
Details
Can be used to estimate either the LOD score or recombination frequency, depending on the value of LOD. Genotype coding must represent dosage of a founder haplotype. For BC populations, possible allele dosages are 0,1. For DH and RIL pops, it is 0,2. For F2 and S1 pops, it is 0,1,2.
Value
If adjacent is FALSE, a matrix of recombination frequencies or LOD scores; otherwise, a three-column data frame with marker, the LOD or r value, and the phase ("c","r") with the previous marker
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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