cash-orderLG: BC, FS and IC method: Order linkage groups

In tpbilton/GUSMap: Genotyping Uncertainty with Sequencing Data and Linkage Mapping (GUSMap)

BC, FS and IC method: Order linkage groups

Description

Method for ordering markers in a linkage group

Usage

BCobj$orderLG(chrom = NULL, mapfun = "haldane", weight="LOD2", ndim=30)
FSobj$orderLG(chrom = NULL, mapfun = "haldane", weight="LOD2", ndim=30)
ICobj$orderLG(chrom = NULL, mapfun = "haldane", weight="LOD2", ndim=30)

Arguments

chrom	An integer vector of the indices for the linkage group(s) that are to be ordered.
mapfun	A character value for the mapping function to be used. For a list of available mapping functions, see mfun.
weight	A character value for the weight function to be used. Can be either "none", "LOD" or "LOD2".
ndim	A integer value for the number of dimensions to use in the unconstrained MDS step.

Details

Linkage groups are ordered using the multidimensional scaling (MDS) approach described by \insertCitepreedy2016tag;textualGUSMap. In brief, the MDS approach starts by performing weighted unconstrained MDS on the matrix of genetic map distances, where the dimension of the weighted unconstrained MDS is controlled by the ndim argument. In the second step, a principal curve is fitted and the projection of the markers into the first principal curve gives the marker order.

BC object: The pseudo-testcross linkage groups with BI SNPs created from the $addBIsnps function are ordered by this function. If the pseudo-testcross linkage groups do not have any BI SNPs, then the ordering is performed on the pseudo-testcross linkage groups created by the $createLG function.

FS object: The combined linkage groups created from the $addBIsnps function are ordered using this function.

IC object: The linkage groups created from the $createLG function are ordered using this function.

There are three different types weigthing matrix that can be used:

• No weights "none": The weight of each SNP pair is set to 1 with the expection that the weights between a MI and PI pair are set to 0 since there is not information of recombination in these SNP pairs.

• LOD score "LOD": The weighting matrix corresponds to the matrix of pairwise LOD scores.

• Squared LOD scores "LOD":The weighting matrix corresponds to the matrix of squared pairwise LOD scores.

Author(s)

Timothy P. Bilton. Code adapted from some R functions associated with the \insertCitepreedy2016tag;textualGUSMap.

References

\insertRef

preedy2016tagGUSMap

See Also

BC, FS, IC, mfun

Examples

## Simulate some sequencing data
set.seed(6745)
config <- list(list(sample(c(1,2,4), size=30, replace=TRUE)))
F1data <- simFS(0.01, config=config, meanDepth=10, nInd=50) 
## Compute 2-point recombination fractions
F1data$rf_2pt()
## create paternal and maternal linkage groups
F1data$createLG()
## Add the BI SNPs
F1data$addBIsnps()

## Order Linkage groups
F1data$orderLG(ndim=5)

tpbilton/GUSMap documentation built on Feb. 22, 2025, 12:27 p.m.