imputeMissingValues: Imputing log2 ratios
Description
Imputing log2 ratios
Usage
imputeMissingValues(seg, chrominfo = chrominfo.Mb, maxChrom =
23, smooth = 0.1)
Arguments
chrominfo
a chromosomal information associated with the mapping of the data
maxChrom
Highest chromosome to impute
smooth
smoothing parameter for the lowess procedure
Value
Computes and returns the imputed log2 ratio matrix of the aCGH object.
Details
There are two main reasons to impute data.
One is that given that imputation is reasonable,
one can increase the analytical power and improve results.
Another, more practical, is that at the moment many widely used
functions in R do not support missing values.
While procedures such as kNN imputations is widely used for gene
expression data, it is more powerful to take advantage of the
genomic structure of the array CGH data and use a smoother.
Note that we perform only one pass of smoothing.
If there still remain missing values, they are imputed by the
median on the chromosome or chromosomal arm where applicable.