nem.discretize: Discretize perturbation data according to control experiments

In nem: (Dynamic) Nested Effects Models and Deterministic Effects Propagation Networks to reconstruct phenotypic hierarchies

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])   

nem documentation built on Oct. 31, 2019, 2:12 a.m.