fixSW: Fixing Switch Errors

In hsphase: Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events Identification of Half-sib Families Using SNP Data

Fixing Switch Errors

Description

Fix switch errors in haplotypes for a half-sib family.

Usage

fixSW(haplotype, ohMax = 0, windowsSize = 100, minLength = 100, cpus = 2)

Arguments

haplotype	matrix. Haplotypes for a half-sib family (two rows per individual).
ohMax	integer. Maximum tolerated opposing homozygotes when grouping each partition (increase if genotyping errors exist).
windowsSize	integer. Partition size (number of SNPs).
minLength	integer. Minimum length between switches.
cpus	integer. Number of CPU threads.

Value

A haplotype matrix with switch errors corrected.

See Also

groupMatSingle and addSwitch

Examples

haplotype <- .simulateHalfsib(7, 2500, type = "haplotype")$phased
switches <- list(500,0,0,1200,c(1000,2000),500,1200)

haplotype2 <- addSwitch(haplotype, switches, 0)

gMat <- groupMatSingle(haplotype2, 100, 2, "haplotype")
imageplot(gMat, title = "Before fixing switches")

haplotype3 <- fixSW(haplotype2, 0, 100, 100)

gMat2 <- groupMatSingle(haplotype3, 100, 2, "haplotype")
imageplot(gMat2, title = "After fixing switches")

hsphase documentation built on Feb. 17, 2026, 5:07 p.m.