discretize.tscores {macat} | R Documentation |
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.
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(stjd) # simple scoring with short running time scores = evalScoring(stjd, "T", 1, nperms=100, cross.validate=FALSE) discrete = discretize.tscores(scores)