nem.discretize {nem} | R Documentation

## Discretize perturbation data according to control experiments

### Description

discretizes raw data to define effects of interventions with respect to wildtype/control measurements

### Usage

    nem.discretize(D,neg.control=NULL,pos.control=NULL,nfold=2,cutoff=0:10/10, pCounts=20, 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
`cutoff` | a (vector of) cutoff value(s) weighting the pos. controls versus the neg. controls. Default: 0:10/10
`pCounts` | pseudo-counts to guard against unreasonable low error estimates
`empPval` | empirical p-value cutoff for effects if only one control is available
`verbose` | Default: TRUE

### Details

Chooses cutoff such that separation between negative and positive controls becomes optimal.

### Value

`dat` | discretized data matrix
`pos` | discretized positive controls [in the two-controls setting]
`neg` | discretized negative controls [in the two-controls setting]
`sel` | effect reporters selected [in the two-controls setting]
`cutoff` | error rates for different cutoff values [in the two-controls setting]
`para` | estimated error rates [in the two-controls setting]

### 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

       # discretize Boutros data as in
       # Markowetz et al, 2005
       data("BoutrosRNAi2002")
       disc <- nem.discretize(BoutrosRNAiExpression,neg.control=1:4,pos.control=5:8,cutoff=.7)
       stopifnot(disc$dat==BoutrosRNAiDiscrete[,9:16])

[Package nem version 2.58.0 Index]