hbp {hsphase} | R Documentation |
Haplotype Blocks of Phased Data
Description
Creates a blocking structure matrix of the half-sib family based on phased data of the sire and half-sib family.
Usage
hbp(PhasedGenotypeMatrix, PhasedSireGenotype, strand = "auto")
Arguments
PhasedGenotypeMatrix |
|
PhasedSireGenotype |
|
strand |
|
Value
Returns a matrix where 3 or 4 stands for the SNP originating in, respectively, strands 1 and 2. 0 indicates that the source strand for the SNP is unknown.
Note
The input matrices must only contain individuals from one half-sib family and one ordered chromosome.
The strand
option should be set to "auto" (default value).
See Also
Examples
sire <- matrix(c(
0,0,0,0,0,1, # Haplotype one of the sire
0,1,1,1,1,0 # Haplotype two of the sire
), byrow = TRUE, ncol = 6)
haplotypeHalfsib <- matrix(c(
1,0,1,1,1,1, # Individual one, haplotype one
0,1,0,0,0,0, # Individual one, haplotype two
0,1,1,0,1,1, # Individual two, haplotype one
1,0,0,1,0,0 # Individual two, haplotype two
), byrow = TRUE, ncol = 6) # 0s and 1s are alelle a and b
hbp(haplotypeHalfsib, sire)
[Package hsphase version 2.0.3 Index]