vector012matrix: multiplication from left of 012 vector with a matrix
In miraculix: Algebraic and Statistical Functions for Genetics

Description Usage Arguments Value Author(s) See Also Examples

vector012matrix and matrixvector012 multiply a real-valued matrix from left and right with a vector that contains only the values 0,1,2, respectively. For larger matrices (greater than 25\times 25) the functions are 3 to 10 times faster than the matrix multiplication %*%.

This function is not based on RFoptions()$genetics$snpcoding.

1 2	vector012matrix(v, M) matrixvector012(M, v)

`v`	an integer valued with values 0,1,2 only. Anything different from 1 and 2 is treated as 0.
`M`	a real-valued matrix whose size matches `v`

The two function vector012matrix and matrixvector012 return a vector of length ncol(M) and nrow(M), respectively.

Martin Schlather, schlather@math.uni-mannheim.de

vectorGeno

relationshipMatrix

set.seed(0)

n <- 800
m <- 800

vl <- sample(0:2, m, replace = TRUE) 
vr <- sample(0:2, n, replace = TRUE)
M <- matrix(1 : (n * m), ncol=n) + 0.0

## v1 and v2 are the same
v1 <- M %*% vr
v2 <- matrixvector012(M, vr)
stopifnot(all(v1 == v2))

## v1 and v2 are the same
v1 <- vl %*% M 
v2 <- vector012matrix(vl, M)
stopifnot(all(v1 == v2))

## matrixvector012 is 3 to 15 times faster for larger matrices
N <- 1 + as.integer(100000000 / n^2)
print(system.time( for (i in 1:N) M %*% vr ))
print(system.time( for (i in 1:N) matrixvector012(M, vr) )) # much faster




## vector012matrix is 3 to 10 times faster for larger matrices
print(system.time(for (i in 1:N) vl %*% M ))
print(system.time( for (i in 1:N) vector012matrix(vl, M) )) # much faster