backtransformAffine: Reverse affine transformation

In HenrikBengtsson/aroma.light-BioC_release: Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types

Description

Reverse affine transformation.

Usage

## S3 method for class 'matrix'
backtransformAffine(X, a=NULL, b=NULL, project=FALSE, ...)

Arguments

X	An NxK matrix containing data to be backtransformed.
a	A scalar, vector, a matrix, or a list. First, if a list, it is assumed to contained the elements a and b, which are the used as if they were passed as seperate arguments. If a vector, a matrix of size NxK is created which is then filled row by row with the values in the vector. Commonly, the vector is of length K, which means that the matrix will consist of copies of this vector stacked on top of each other. If a matrix, a matrix of size NxK is created which is then filled column by column with the values in the matrix (collected column by column. Commonly, the matrix is of size NxK, or NxL with L < K and then the resulting matrix consists of copies sitting next to each other. The resulting NxK matrix is subtracted from the NxK matrix X.
b	A scalar, vector, a matrix. A NxK matrix is created from this argument. For details see argument a. The NxK matrix X-a is divided by the resulting NxK matrix.
project	returned (K values per data point are returned). If TRUE, the backtransformed values "(X-a)/b" are projected onto the line L(a,b) so that all columns will be identical.
...	Not used.

Value

The "(X-a)/b" backtransformed NxK matrix is returned. If project is TRUE, an Nx1 matrix is returned, because all columns are identical anyway.

Missing values

Missing values remain missing values. If projected, data points that contain missing values are projected without these.

Examples

X <- matrix(1:8, nrow=4, ncol=2)
X[2,2] <- NA

print(X)

# Returns a 4x2 matrix
print(backtransformAffine(X, a=c(1,5)))

# Returns a 4x2 matrix
print(backtransformAffine(X, b=c(1,1/2)))

# Returns a 4x2 matrix
print(backtransformAffine(X, a=matrix(1:4,ncol=1)))

# Returns a 4x2 matrix
print(backtransformAffine(X, a=matrix(1:3,ncol=1)))

# Returns a 4x2 matrix
print(backtransformAffine(X, a=matrix(1:2,ncol=1), b=c(1,2)))

# Returns a 4x1 matrix
print(backtransformAffine(X, b=c(1,1/2), project=TRUE))

# If the columns of X are identical, and a identity
# backtransformation is applied and projected, the
# same matrix is returned.
X <- matrix(1:4, nrow=4, ncol=3)
Y <- backtransformAffine(X, b=c(1,1,1), project=TRUE)
print(X)
print(Y)
stopifnot(sum(X[,1]-Y) <= .Machine$double.eps)


# If the columns of X are identical, and a identity
# backtransformation is applied and projected, the
# same matrix is returned.
X <- matrix(1:4, nrow=4, ncol=3)
X[,2] <- X[,2]*2; X[,3] <- X[,3]*3;
print(X)
Y <- backtransformAffine(X, b=c(1,2,3))
print(Y)
Y <- backtransformAffine(X, b=c(1,2,3), project=TRUE)
print(Y)
stopifnot(sum(X[,1]-Y) <= .Machine$double.eps)

HenrikBengtsson/aroma.light-BioC_release documentation built on May 7, 2019, 1:55 a.m.