fill.NA {Mfuzz}R Documentation

Replacement of missing values

Description

Methods for replacement of replacing missing values. Missing values should be indicted by NA in the expression matrix.

Usage

fill.NA(eset,mode="mean",k=10)

Arguments

eset object of the class exprSet
mode method for replacement of missing values:
  • mean- missing values will be replaced by the mean expression value of the gene,
  • median- missing values will be replaced by the median expression value of the gene,
  • knn- missing values will be replaced by the averging over the correponding expression values of the k-nearest neighbours,
  • knnw-same replacement method as knn, but the expression values averaged are weighted by the distance to the correponding neighbour
k Number of neighbours, if one of the knn method for replacement is chosen (knn,knnw).

Value

The function produces an object of theexprSet class with missing values replaced.

Note

The replacement methods knn and knnw can computationally intensive for large gene expression data sets. It may be a good idea to run these methods as a ‘lunchtime’ or ‘overnight’ job.

Author(s)

Matthias E. Futschik (http://itb.biologie.hu-berlin.de/~futschik) and Lokesh Kumar

Examples

if (interactive()){
data(yeast) # data set includes 17 measurements
yeastF <- filter.NA(yeast) 
yeastF <- fill.NA(yeastF)
}

[Package Mfuzz version 1.6.0 Index]