Usage
scoreOrderComparison(exprs1, labels1, paired1, exprs2, labels2, paired2, test.method = test.z, nn, bases, two.sided, empirical)
scoreOrderComparisonBoth(exprs1, labels1, paired1, exprs2, labels2, paired2, test.method = test.z, nn, bases, two.sided, empirical)
Arguments
exprs1,exprs2
gene expression matrices.
labels1,labels2
class labels, one label per column in matrices.
paired1,paired2
logical, whether samples are paired in classes.
test.method
a function computing one test statistics per row and taking
a matrix, a label vector and a logical for pairing as parameters.
Valid examples are test.fc, test.t and test.z.
nn
a vector of rank limits. The score is computed taking into
account ranks up to these limits only. One limit per entry in bases.
bases
a vector of bases used in weighted scores, is equal to exp(-alpha).
The function can compute scores for several regularization parameters in one go.
two.sided
if TRUE both ends of the lists are taken into account, only
top ranks are considered otherwise.