haplomatrix.class: Class 'haplomatrix'

In miraculix: Algebraic and Statistical Functions for Genetics

Description

Class representing a haplo matrix

Usage

## S3 method for class 'haplomatrix'
print(x, ...)
## S3 method for class 'haplomatrix'
str(object, ...)
## S3 method for class 'haplomatrix'
as.matrix(x, ...)

Arguments

x,object	a compressed (SNP x Individuals) matrix
...	see print, str for their options. The command as.matrix has the following options indiv vector of integer, indicating individuals to be extracted sets value 1, 2 or 1:2. Indicates the chromosome set to be returned. Default:1:2 IndividualsPerColumn \ipc Default: TRUE DoubledIndividuals \dindiv Default: TRUE

Details

Since the haplo matrix takes only the values 0 and 1, haplomatrix uses a one bit compressed storing mode. A haplomatrix can quickly be transformed into a genomicmatrix (by exactly this command) in case of the default two-bit coding, e.g. RFoptions(snpcoding=Shuffle).

See Also

genomicmatrix-class

Examples

set.seed(0)
indiv <- 5
loci <- 4
M <- matrix(sample(0:1, 2 * indiv * loci, replace=TRUE), nrow = loci)
str(M)

GM <- haplomatrix(M)
print(GM)
str(GM)
print(as.matrix(GM))
print(as.matrix(GM, indiv=2:4, sets=1))
stopifnot(sum(abs(as.matrix(GM) - M)) == 0)

miraculix documentation built on Sept. 22, 2021, 5:07 p.m.