GeneRanking-class: "GeneRanking"
Description
Object returned by all implemented ranking methods (RankingTstat, RankingFC, RankingWelchT, RankingWilcoxon,
RankingBaldiLong, RankingFoxDimmic, RankingLimma,
RankingEbam, RankingWilcEbam, RankingSam, RankingShrinkageT, RankingSoftthresholdT,
RankingPermutation).Slots
x:- Gene expression
matrix rows correspond to genes, columns to samples (arrays). y:- A two-level
factor of class labels. statistic:- A
numeric vector storing the test statistics. ranking:- The ranking is determined via the statistic (normally via the size of absolute value).
The lower the rank, the higher the magnitude of differential expression.
There is no distinction of over- and underexpression.
pval:- The vector of p-values computed from
statistic.
NA if p-values 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
- Use
summary(GeneRanking-object) for a five-point-summary of statistics and p-values arranged as two-column table. The second column (p-values) are NA
in the case that p-values have not been computed. - toplist
- Use
toplist(object, k=10)
to get information about the top k=10 genes.