| topgenes {made4} | R Documentation |
topgenes will return a list of the top N variables from the positive, negative or both ends of an
axis. That is, it returns a list of variables that have the maximum and/or minimum values in
a vector.
topgenes(x, n = 10, axis = 1, labels = row.names(x), ends = "both", ...)
x |
A vector, matrix or
data.frame. Typically a data frame $co or $li
from dudi or $ls, $li, $co from
bga. |
n |
An integer indicating the number of variables to be returned. Default is 5. |
axis |
An integer indicating the column of x. Default is 1 (first axis, of $co or $li file) |
labels |
A vector of row names, for x[,axis]. Default values is row.names(x) |
ends |
A string, "both", "neg", "pos", indicating whether variable label should be return from both, the negative or the positive end of an axis. The default is both. |
... |
further arguments passed to or from other methods |
topgenes calls genes1d. genes1d is similar to
genes, but returns an index of genes at the ends of
one axis not two axes. Given a $co or $li file it will return that variables at the ends of the axis.
Returns a vector or list of vectors.
AedinCulhane
See Also as genes
# Simple example
a<-rnorm(50)
order(a)
topgenes(a, labels=c(1:length(a)), ends="neg")
# Applied example
data(khan)
if (require(ade4, quiet = TRUE)) {
khan.coa<-dudi.coa(khan$train[1:100,1:10], scannf=FALSE, nf=2)
}
ind<-topgenes(khan.coa$li, ends="pos")
ind.ID<-topgenes(khan.coa$li, ends="pos", labels=khan$gene.labels.imagesID)
ind.symbol<-topgenes(khan.coa$li, ends="pos", labels=khan$annotation$Symbol)
Top10.pos<- cbind("Gene Symbol"=ind.symbol,
"Clone ID"=ind.ID, "Coordinates"=khan.coa$li[ind,], row.names=c(1:length(ind)))
Top10.pos