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 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.
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)