nem.cont.preprocess {nem} | R Documentation

## Calculate classification probabilities of perturbation data according to control experiments

### Description

Calculates probabilities of data to define effects of interventions with respect to wildtype/control measurements

### Usage

    nem.cont.preprocess(D,neg.control=NULL,pos.control=NULL,nfold=2, influencefactor=NULL, empPval=.05, verbose=TRUE)

### Arguments

`D` | matrix with experiments as columns and effect reporters as rows
`neg.control` | either indices of columns in `D` or a matrix with the same number of rows as `D`
`pos.control` | either indices of columns in `D` or a matrix with the same number of rows as `D`
`nfold` | fold-change between neg. and pos. controls for selecting effect reporters. Default: 2
`influencefactor` | factor multiplied onto the probabilities, so that all negative control genes are treated as influenced, usually automatically determined
`empPval` | empirical p-value cutoff for effects if only one control is available
`verbose` | Default: TRUE

### Details

Determines the empirical distributions of the controls and calculates the probabilities of pertubartion data to belong to the control distribution(s).

### Value

`dat` | data matrix
`pos` | positive controls [in the two-controls setting]
`neg` | negative controls [in the two-controls setting]
`sel` | effect reporters selected [in the two-controls setting]
`prob.influenced` | probability of a reporter to be influenced
`influencefactor` | factor multiplied onto the probabilities, so that all negative control genes are treated as influenced

### Note

preliminary! will be developed to be more generally applicable

### Author(s)

Florian Markowetz

### References

Markowetz F, Bloch J, Spang R, Non-transcriptional pathway features reconstructed from secondary effects of RNA interference, Bioinformatics, 2005

### See Also

`BoutrosRNAi2002`

### Examples

       data("BoutrosRNAi2002")
       preprocessed <- nem.cont.preprocess(BoutrosRNAiExpression,neg.control=1:4,pos.control=5:8)

[Package nem version 2.56.0 Index]