GeneSelector (version 2.22.0)

GenerateFoldMatrix: Altered datasets via k-Jackknife or label exchange

Description

Generates an object of class FoldMatrix to be used for RepeatRanking.

Usage

GenerateFoldMatrix(x, y, k = 1, replicates = ifelse(k==1, length(y), 10), type = c("unpaired", "paired", "onesample"), minclassize = 2, balanced = FALSE, control)

Arguments

x

Only needed if y is stored within an ExpressionSet.

y

y may be a numeric vector or a factor with at most two levels. If x is an ExpressionSet, then y is a character specifying the phenotype variable in the output from pData. If type = "paired", take care that the coding is correct.

k

Number of observations that are removed or whose labels are exchanged. Label exchange means that the observed label is replaced by the label of the other class (s. RepeatRanking).

replicates

Number of replications if k>1.

type

One of "paired", "unpaired", "onesample", depends on the type of test to be performed, s. for example RankingTstat.

minclassize

If minclassize=k for some integer k, then the number of observations in each class are grater then or equal to minclassize for each replication.

balanced

If balanced=TRUE, then the proportions of the two classes are (at least approximately) the same for each replication. It is a shortcut for a certain value of minclasssize. May not be reasonable if class proportions in the given dataset are unbalanced in the original sample.

control

Further control arguments concerning the generation process of the fold matrix, s. samplingcontrol.

Value

FoldMatrix.

warning

If the generation process (partially) fails, try to reduce the constraints or change the argument control.

References

Davison, A.C., Hinkley, D.V. (1997) Bootstrap Methods and their Application. Cambridge University Press

See Also

GenerateBootMatrix, RepeatRanking

Examples

 ## Load toy gene expression data
data(toydata)
### class labels
yy <- toydata[1,]
### Generate Leave-One-Out / Exchange-One-Label matrix
loo <- GenerateFoldMatrix(y = yy, k=1)
### A more complex example
l3o <- GenerateFoldMatrix(y = yy, k=3, replicates=30, minclassize=5)