discretize_tscores: Discretize regularized t-scores
In macat: MicroArray Chromosome Analysis Tool

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

discretize.tscores returns a discretized version of the scores in the MACATevalScoring object. Discretization is performed by comparing the value gene-wise (location-wise) 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.

1 2	discretize.tscores(scores) discretizeAllClasses.tscores(data, chrom, nperms=10, kernel=rbf, kernelparams=NULL, step.width=100000)

`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

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.

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

The MACAT development team

evalScoring, kernels, pythondata

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