geno: Manipulating Compressed Matrices

In miraculix: Algebraic and Statistical Functions for Genetics

Description

copyGeno copies a coded SNP matrix zeroNthGeno writes zeros into selected rows of a coded SNP matrix fillGeno allows to fill (or replace) colums of a compressed (snps \times indiv) matrix.

Usage

fillGeno(SNPxIndiv, indiv, values, IndividualsPerColumn=TRUE,
         DoubledIndividuals=TRUE)
copyGeno(SNPxIndiv)
zeroNthGeno(SNPxIndiv, snps)

Arguments

SNPxIndiv	a compressed SNP (genotype) vector or matrix, obtained from genomicmatrix or haplomatrix
indiv	integer vector. It gives the columns of the (SNP \times Indiv) matrix that has to be filled with values
values	coded or uncoded vector or matrix of haplotype or genotypes.
snps	vector of integers, which gives the selected rows. If missing all rows are selected.
IndividualsPerColumn	\ipc
DoubledIndividuals	\dindiv

Value

All functions return a compressed SNP matrix of class genomicmatrix.

See Also

genomicmatrix-class

vectorGeno for multiplying a vector from the left

genoVector for multiplying a vector from the right

Examples

 
require(RandomFieldsUtils)
set.seed(0)

indiv <- sample(1000, 1)
snps <- indiv * 2^sample(7,1)
M <- matrix(nrow = snps, sample(0:2, snps * indiv, replace=TRUE))
storage.mode(M) <- sample(c("integer", "double"), 1)
CM <- genomicmatrix(M)
str(CM)
Z <- as.matrix(CM)
Print(M, CM, Z)
stopifnot(all(M == Z))

N <- sample(snps, snps / 4)
Z1 <- as.matrix(CM, snps=N)
stopifnot(all(M[N, ] == Z1))

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