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 1.2.0 Index]