cash-createLG: BC, FS and IC method: Create linkage groups

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

BC, FS and IC method: Create linkage groups

Description

Method for creating linkage groups using the computed LOD scores.

Usage

BCobj$createLG(parent = "both", LODthres = 10, nComp = 10, reset = FALSE)
FSobj$createLG(parent = "both", LODthres = 10, nComp = 10, reset = FALSE)
ICobj$createLG(LODthres = 10, nComp = 10)

Arguments

parent	A character vector specifying whether to create linakge groups using the maternal-informative (MI) SNPs ("maternal"), the paternal-informative (PI) SNPs ("paternal"), or both the MI and PI SNPs ("both").
LODthres	A positive numeric value specifying the LOD threshold used to add SNPs to the linkage groups.
nComp	A positive integer value specifying how many SNPs in the linakge group to compute the average LOD score with the unmapped SNP.
reset	Logical value specifying whether to reset the linkage groups and linkage maps computed using the $addBIsnps, $computeMap and $orderLG functions.

Details

Linkage groups are formed using the following algorithm

1. The two unmapped SNPs (e.g. not already in a linkage group) with the highest LOD score are grouped together to form a linkage group.

2. The average LOD score between each unmapped SNP and a specified number (nComp) of SNPs in the linkage group that have the highest LOD score with the unmapped SNP is computed. The unmapped SNP with the largest average LOD score is mapped to the linkage group if the average LOD score is above the LOD threshold (given by LODthres).

3. When no more SNPs are added to the linkage group, repeat steps 1-2 to form a new linkage group.

4. Stop no more linkage groups can be formed or all the SNPs have been mapped to a linkage group.

The performance of the linkage group algorithm depends on the value of LODthres and nComp. The user is advised to experiment with different values and examine the matrix of recombination fraction estimates (using the $plotLG function).

Notes:

• The LOD scores used in this function are computed using the $rf_2pt which needs to be run beforehand.

• A MI linkage group is one which only contains MI SNPs and a PI linkage group is one with only PI SNPs. These linkage groups are referred to as the "puesdo-testcross linkage groups".

• For BC and FS objects, only MI and PI SNPs are used to construct linkage groups. The SI SNPs inferred in the makeBC or makeFS function when the argument inferSNPs = TRUE are not used in the $createLG function. For an IC object, all the inferred BI SNPs are used to construct linkage groups.

Author(s)

Timothy P. Bilton

See Also

BC, FS, IC

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(nClust=1)

## create paternal and maternal linkage groups
F1data$createLG()

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