cash-removeSNP: BC, FS and IC method: Remove SNP from linkage groups

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

BC, FS and IC method: Remove SNP from linkage groups

Description

Method for removing SNPs from linkage groups in an BC, FS or IC object.

Usage

BCobj$removeSNP(snps, where = NULL)
FSobj$removeSNP(snps, where = NULL)
ICobj$removeSNP(snps)

Arguments

snps	An integer vector giving the indices of the SNP to be removed.
where	Character vector specifying which set of linkage groups to remove SNPs from (see details).

Details

For a linkage analysis in GUSMap, there may be a need to delete 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. More than one linkage group can be deleted at once.

Note: When the linkage group(s) are deleted, the indices of the remaining linkage groups changes. Print the BC, FS or IC object to investiage what these are after running this function.

BC object: When where = "LG-pts", SNPs 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 SNPs from the set of pseudo-testcross linkage groups with BI SNPs added created from the $addBIsnps function will be removed. When where = NULL, SNPs 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", SNPs 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 SNPs from the set of combined linkage groups created from the $addBIsnps function will be removed. When where = NULL, SNPs 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 some sequencing data
set.seed(6745)
config <- list(list(sample(c(1,2,4), size=20, 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()

## Remove SNPs 3,7,15,20 from the linkage groups
F1data$removeSNP(snps = c(3,7,15,20))

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