| orderFeatures {hddplot} | R Documentation |
For each row of data, an F or (potentially) other
statistic is calculated, using the function FUN, that measures
the extent to which this variable separates the data into groups. This
statistic is then used to order the rows.
orderFeatures(x, cl, subset = NULL, FUN = aovFbyrow, values = FALSE)
x |
Matrix; rows are features, and columns are observations ('samples') |
cl |
Factor that classifies columns into groups |
subset |
allows specification of a subset of the columns of data |
FUN |
specifies the function used to measure separation between groups |
values |
if TRUE, F-values as well as the ordering are returned |
Either (values=FALSE) a vector that orders the rows,
or (values=TRUE)
ord |
a vector that orders the rows |
stat |
ordered values of the statistic |
John Maindonald
~~objects to See Also as help, ~~~
mat <- matrix(rnorm(1000), ncol=20)
cl <- factor(rep(1:3, c(7,9,4)))
ord <- orderFeatures(mat, cl)
## The function is currently defined as
function(x, cl, subset=NULL, FUN=aovFbyrow, values=FALSE){
if(dim(x)[2]!=length(cl))stop(paste("Dimension 2 of x is",
dim(x)[2], "differs from the length of cl (=",
length(cl)))
## Ensure that cl is a factor & has no redundant levels
if(is.null(subset))
cl <- factor(cl)
else
cl <- factor(cl[subset])
if(is.null(subset))
stat <- FUN(x, cl)
else
stat <- FUN(x[, subset], cl)
ord <- order(-abs(stat))
if(!values)ord else(list(ord=ord, stat=stat[ord]))
}