Description Usage Arguments Details Value Author(s) See Also Examples
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.
1 |
x |
A |
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | # 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<-ord(khan$train[1:100,])}
ind<-topgenes(khan.coa, ends="pos")
ind.ID<-topgenes(khan.coa, ends="pos", labels=khan$gene.labels.imagesID)
ind.symbol<-topgenes(khan.coa, ends="pos", labels=khan$annotation$Symbol)
Top10.pos<- cbind("Gene Symbol"=ind.symbol,
"Clone ID"=ind.ID, "Coordinates"=khan.coa$ord$li[ind,], row.names=c(1:length(ind)))
Top10.pos
|
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