discretize_tscores: Discretize regularized t-scores

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

Description

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.

Usage

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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

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  #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)

macat documentation built on Nov. 1, 2018, 2:34 a.m.