cash-maskSNP: BC, FS and IC method: Mask and unmask SNPs

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

BC, FS and IC method: Mask and unmask SNPs

Description

Method for masking and unmasking SNPs in an BC, FS or IC object.

Usage

BCobj$maskSNP(snps)
FSobj$maskSNP(snps)
ICobj$maskSNP(snps)

BCobj$unmaskSNP(snps)
FSobj$unmaskSNP(snps)
ICobj$unmaskSNP(snps)

Arguments

snps	An integer vector giving the indices of the SNP(s) in the dataset.

Details

In the linkage mapping process, some SNPs are often probmatic and there may be the need exclude these SNPs in forming linkage groups and computing linkage maps. This can be achieved using the $maskSNP function, which masks SNPs. Once a SNP is masked, it will be ignored in the functions $createLG, $addBIsnps, $computeMap. Note, however, that if a SNP is already included in a linkage group, masking a SNP will not remove it (To remove SNPs from a linkage group, one needs to use the $removeSNP function).

The $unmaskSNP function just unmasks any SNPs which have been masked using $maskSNP.

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)

## Mask SNPs 1,5,8,11,13
F1data$maskSNP(c(1,5,8,11))

## Unmask SNPs 5 and 8
F1data$unmaskSNP(c(5,8))

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