center_ddepn: Perform centering of single replicate time courses.

In ddepn: Dynamic Deterministic Effects Propagation Networks: Infer signalling networks for timecourse RPPA data.

Description

For each experiment in a data matrix (i.e. stimulation/inhibition) subtract the median of the curve and shift up to the median of the whole experiment, i.e. median of all biological and technical replicates.

Usage

center_ddepn(dat)

Arguments

dat	The data matrix obtained in hcc1954raw, after fcf normalisation. See examples for how to fcf normalise and center the data.

Details

Used to center the replicate time courses. The time curves should lie as close together as possible, so that the estimated active/passive Gaussians estimated in ddepn are not obfuscated by the variance between the replicates. FCF normalising and centering will yield the data matrix obtained in hcc1954. The function is provided for convenience. It should be traceable, how the matrices were generated.

Value

The centered data matrix.

Author(s)

Christian Bender

See Also

ddepn hcc1954 hcc1954raw

Examples

## Not run: 
library(ddepn)
data(hcc1954raw)

## perform FCF normalisation
datfcf <- hcc1954raw / hcc1954fcf * hcc1954fcfmedian

## center the data
datc <- center_ddepn(datfcf)

## End(Not run)

ddepn documentation built on May 2, 2019, 4:42 p.m.