scoreOrderComparison: Score the Comparison of two Gene Rankings
In OrderedList: Similarities of Ordered Gene Lists

Description Usage Arguments Details Value Author(s)

Compute weighted similarity score for gene rankings determined via the chosen test statistics.

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)

`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.

scoreOrderComparison computes scores only for the direct comparison. scoreOrderComparisonBoth in addition computes scores for reversed orders, i.e., one of the rankings is reversed.

For each entry in bases, thus for each regularization parameter alpha, one score is returned in an array.

Claudio Lottaz

OrderedList documentation built on Nov. 8, 2020, 5:41 p.m.