"GeneRanking"

Description

Object returned by all implemented Ranking methods (RankingTstat,RankingFC, RankingWelchT, RankingWilcoxon, RankingBaldiLong, RankingFoxDimmic, RankingLimma, RankingEbam, RankingWilcEbam, RankingSam, RankingBstat, RankingShrinkageT, RankingSoftthresholdT, RankingPermutation, RankingGap)

Slots

x:

A matrix storing gene expression, rows correspond to genes, columns to samples (arrays).

y:

A factor with two levels of class labels.

statistic:

A numeric vector storing the statistics, ordered according to the ranking.

ranking:

A vector of indices that represents the ranking of the genes. The first entry corresponds to the best one. The ranking is determined via the statistic (size of absolute value), so there is no distinction of over- and underexpression. For example, if there are five genes with indices 1,2,3,4,5, ranking=3,4,2,1,5 means that the gene with index 3 is ranked highest, having the largest statisitic (in absolze value), gene 4 has rank 2, and so on.

pval:

The ordered vector of p-values.
NA if pvalues have not been computed.

type:

Type of the test (one of "unpaired", "paired", "onesample").

method:

Short name of the ranking Method.

Methods

show

Use show(GeneRanking-object) for brief information.

summary,GeneRanking

Use summary(GeneRanking-object) For a five-point-summary of statistics and p-values.

toplist

Use toplist(object, k=10) to get information about the top k=10 genes.

Author(s)

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

See Also

RepeatRanking, GetRepeatRanking