discretize.tscores {macat}R Documentation

Discretize regularized t-scores

Description

discretize.tscores returns a discretized version of the scores in the MACATevalScoring object. Discretization is performed by comparing the value genewise (locationwise) with the symmetric upper and lower quantile given by margin (in percent margin/2 lower and upper quantile). discretizeAllClasses produces a flatfile readable by PYTHON.

Usage

discretize.tscores(scores)
discretizeAllClasses.tscores(data, chrom, nperms=10, kernel=rbf, kernelparams=NULL, step.width=100000)

Arguments

scores a MACATevalScoring object obtained from evalScoring
data a MACATData Object containing all expression values, geneLocations and labels (obtained from preprocessedLoader)
chrom chromosome that is discretized
nperms number of permutations for the computation of empirical p values (evalScoring)
kernel kernel function used for smoothing one of rbf, kNN, basePairDistance or your own
kernelparams list of parameters for the kernels
step.width size of a interpolation step in basepairs

Details

The filename for the python flat files are discrete_chrom_<chrom>_class_<label>.py where <chrom> and <label> are the names of the chromosome and class label.

Value

discretize.tscores a vector of discretized tscores
discretizeAllClasses.tscores creates python flatfiles (see details)

Author(s)

The MACAT development team

See Also

evalScoring, kernels, pythondata

Examples

  #loaddatapkg("stjudem")
  data(stjd)
  # simple scoring with short running time
  scores = evalScoring(stjd, "T", 1, nperms=100, cross.validate=FALSE)
  discrete = discretize.tscores(scores)

[Package macat version 1.6.0 Index]