comp.FC: Computing Fold Change for Differential Expression
Description
comp.FC returns a function of one argument with bindings for
L, is.log and FUN. This function accepts a
microarray data matrix as its single argument, when evaluated, computes
fold change for each row of the matrix.
Usage
comp.FC(L = NULL, is.log = TRUE, FUN = mean)
Arguments
L
A vector of integers corresponding to observation (column)
class labels. For $k$ classes, the labels must be integers
between 0 and $k-1$.
is.log
A logical variable indicating whether the data has been
logged.
FUN
The summary statistics function used to calculate fold
change, the default is set as mean, the user can also
use median
Value
comp.FC returns a function with bindings for L,
is.log and FUN, which calculates and returns a vector of
fold changes for each row in the data matrix.
Details
The function returned by comp.FC calculates fold change for each row
of the matrix, given specific class labels. If is.log=TRUE,
fold change is calculated by subtraction; if is.log=FALSE,
fold change is calculated by division.
X <- matrix(rnorm(1000,0,0.5), nc=10)
L <- rep(0:1,c(5,5))
# genes 1-10 are differentially expressedX[1:10,6:10]<-X[1:10,6:10]+1
f <- comp.FC(L=L)
f.X <- f(X)