"CombinedRanking"

Description

Object returned from a call to GeneSelector.

Slots

ranking:

'Final' ranking, usually obtained by combinining several statistics. The generation of this ranking is described in GeneSelector.
The first entry contains the index of the gene ranked highest, as in GeneRanking.

rankmatrix:

Matrix of rankings, arranged in a way that the rankings from the most important statistic is in column 1. In contrast to ranking, the first row contains the rankings of the gene with the first index. This slot is used rather for internal reasons.

inout:

Matrix arranged in the same way as rankmatrix, but information is now binary: If the specified threshold, then there is a "+" symbolizing selection, whereas a "-" symbolizes removal.

selected:

The indices of those genes that fall below the specified threshold. Can be accessed more conveniently using SelectedGenes

adjpval:

Numeric vector of adjusted p-values, ordered according to ranking. NA if no adjustment has been taken place (in the case that the threshold was fixed by the user).

maxrank:

Threshold rank, either defined by the user or obtained via p-value adjustment.

statistics:

The names of the statistics used, ordered according to their importance (as defined by the user).

absdist:

Absolute (L1) distance from (theoretically) best possible result (rank 1 in all rankings), ordered according to ranking. Note that minimum absdist does not imply best rank and vice versa, because the computed distance does not weigh different statistics differently.

reldist:

A 'normalized' version of absdist (lies in [0;1]).

Methods

show

Use show(object) for brief information.

toplist

Use toplist(object, k=10) to get information about the top k=10 genes.
The ranking used is a synthesis from several statistics.

SelectedGenes

Use SelectedGenes(object) to show all genes that have been selected by the GeneSelector.

GeneInfoScreen

Use GeneInfoScreen, which=1 to get detailed information about the gene with index 1, arranged in a pretty plot.

plot

Use plot(object) to visualize relative distances, s. plot,CombinedRanking

Author(s)

Martin Slawski martin.slawski@campus.lmu.de
Anne-Laure Boulesteix http://www.slcmsr.net/boulesteix