impute.nas.by.surrounding {SIM}R Documentation

Impute NA's in array-CGH data

Description

Replace an NA by the median of the surrounding features in the same sample.

Usage

impute.nas.by.surrounding(dataset, window.size = 5)

Arguments

dataset data.frame with the dataset to replace the NA's by the medians of the surrounding features.
window.size numeric value, specifying of how many features around the NA the median should be taken.

Details

This function can be used when the dependent dataset in the integrated.analysis function is array-CGH data and contains probes that have an NA. To avoid loosing data by throwing away the probes with NA's, the impute.nas.by.surrounding function can be used which simply takes the median of the probes around an NA. The number of probes used for the imputatin is chosen by giving a value for window.size. This script takes quite long to run!

Value

A data.frame is returned, containing the inserted dataset without NA's, which are medianed.

Author(s)

Marten Boetzer, Melle Sieswerda, Renee X. de Menezes R.X.Menezes@lumc.nl

See Also

SIM, assemble.data, integrated.analysis, sim.plot.zscore.heatmap, sim.plot.pvals.on.region, sim.plot.pvals.on.genome, tabulate.pvals, tabulate.top.dep.features, tabulate.top.indep.features, sim.update.chrom.table

Examples


## Not run: cgh.imp <- impute.nas.by.surrounding(cgh)

[Package SIM version 1.10.0 Index]