cash-mergeLG: BC, FS and IC method: Merge linkage groups

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

BC, FS and IC method: Merge linkage groups

Description

Method for merging multiple linkage groups contained in an BC, FS or IC object.

Usage

BCobj$mergeLG(LG, where = NULL, mergeTo = NULL)
FSobj$mergeLG(LG, where = NULL, mergeTo = NULL)
ICobj$mergeLG(LG)

Arguments

LG	An integer vector specifying the indices of the linkage groups to be merged.
where	Character vector specifying which list of linkage groups to merge linkage groups from. "LG-pts" is for the maternal and paternal linkage groups, "LG-bi" is for the pseudo-testcross linkage groups with BI SNPs added (BC objects only) and "LG-comb" is for the combined linkage group list (FS objects only).
mergeTo	Character value specifying whether the merged linkage groups are to be considered as MI linkage groups (maternal) or PI linkage groups (paternal). Only applies in the case of merging pseudo-testcross linkage groups.

Details

For a linkage analysis in GUSMap, there may be the need to merge linkage groups. The indices of the linkage groups corresponds to the number given in the output for the BC, FS or IC object. There needs to be at least two linkage groups specified for merging and more than two linkage groups can be merged at once.

BC object: When where = "LG-pts", MI and PI linkage groups will be merged from the set of pseudo-testcross linkage groups created via the $createLG function. On the other hand, if where = "LG-bi", then linkage groups from the pseudo-testcross linkage groups with BI SNPs created from the $addBIsnps or $orderLGs functions will be merged. When where = NULL, linkage groups will be merged in the set of pseudo-testcross linkage groups with BI SNPs ("LG-pts") if available, otherwise they will be merged in the set of pseudo-testcross linkage groups ("LG-bi").

FS object: When where = "LG-pts", MI and PI linkage groups will be merged from the set of pseudo-testcross linkage groups created via the $createLG function. On the other hand, if where = "LG-comb", then linkage groups from the set of combined linkage groups created from the $addBIsnps function will be merged. When where = NULL, linkage groups will be merged in the set of combined linkage groups ("LG-comb") if available, otherwise they will be merged in the set of pseudo-testcross linkage groups ("LG-bi").

BC and FS objects: In the case when at least one MI linkage group is to be merged with at least one PI linkage group, the second argument (mergeTo) specifies whether the merged linkage groups are to be considered as MI linkage groups (maternal) or PI linkage groups (paternal). Otherwise, the user will be prompted to input which parental line to merge the linkage groups to.

Author(s)

Timothy P. Bilton

See Also

BC, FS, IC

Examples

## simulate sequencing data
set.seed(8932)
config <- list(replicate(2,sample(c(1,2,4), size=30, replace=TRUE), simplify = FALSE))
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$createLG()
## merge linkage groups 1 and 2
F1data$mergeLG(LG = c(1,2))

## create paternal and maternal linkage groups
F1data$createLG()
## merge linkage groups 1 and 3
F1data$mergeLG(LG = c(1,3), mergeTo="paternal")

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