nem.discretize: Discretize perturbation data according to control experiments

Description Usage Arguments Details Value Note Author(s) References See Also Examples

Description

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

Usage

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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

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   # 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])   


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