scale {annmatrix}

Scaling and Centering of annmatrix Objects

Description

Centers and scales the columns of an annmatrix object.

Usage

## S3 method for class 'annmatrix'
scale(x, center = TRUE, scale = TRUE)

Arguments

x

annmatrix object.

center

either a logical value or a numeric vector of length equal to the number of columns of 'x' (default is TRUE).

scale

either a logical value or a numeric vector of length equal to the number of columns of 'x' (default is TRUE).

Details

Behaves exactly as scale on a regular matrix with the preservation of 'annmatrix' class being the only difference.

Value

The centered and/or scaled annmatrix object with additional attributes "scaled:center" and "scaled:scale" holding the numbers used for centering and scaling of each column.

Author(s)

Karolis Koncevičius

See Also

scale.default

Examples

# construct annmatrix object
x <- matrix(rnorm(20*10), 20, 10)

coldata <- data.frame(group  = rep(c("case", "control"), each = 5),
                      gender = sample(c("M", "F"), 10, replace = TRUE))

rowdata <- data.frame(chr = sample(c("chr1", "chr2"), 20, replace = TRUE),
                      pos = runif(20, 0, 1000000))

X <- annmatrix(x, rowdata, coldata)

scale(X)
scale(X, center = colMeans(X))