cash-removeLG: BC, FS and IC method: Remove linkage groups

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

BC, FS and IC method: Remove linkage groups

Description

Method for removing linkage group(s) from the list of linkage groups contained in a BC, FS or IC object.

Usage

BCobj$removeLG(LG, where = NULL)
FSobj$removeLG(LG, where = NULL)
ICobj$removeLG(LG)

Arguments

LG	An integer vector specifying the number of the linkage groups to be removed.
where	Character vector specifying which list of linkage groups to remove linkage groups from. "LG-pts" is for the maternal and paternal pseudo-testcross 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).

Details

For a linkage analysis in GUSMap, there may be the need to remove linkage groups from the list of created linkage groups. The indices of the linkage groups corresponds to the number given in the output for the BC, FS or IC object.

BC object: When where = "LG-pts", linkage groups will be removed from the set of pseudo-testcross linkage groups created via the $createLG function. On the other hand, if where = "LG-bi", then the pseudo-testcross linkage groups with BI SNPs added created from the $addBIsnps function will be removed. When where = NULL, linkage groups will be removed from the set of pseudo-testcross linkage groups with BI SNPs added if available, otherwise they will be removed from the set of pseudo-testcross linkage groups.

FS object: When where = "LG-pts", linkage groups will be removed 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 removed. When where = NULL, linkage groups will be removed from the set of combined linkage groups if available, otherwise they will be removed from the set of pseudo-testcross linkage groups.

Author(s)

Timothy P. Bilton

See Also

BC, FS, IC

Examples

## simulate sequencing data
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()

## remove linkage groups 2 and 4
F1data$removeLG(LG = c(2,4))

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