RepeatedRanking-class: "RepeatedRanking"
Slots
original:- The ranking based on the original data set (output from RepeatRanking) or on a reference
method (output from MergeMethods), represented by an object of class
GeneRanking rankings:- The rankings obtained from altered datasets (output from RepeatRanking or from different methods (output from MergeMethods),
stored as a matrix.
One column represents one replication (output from RepeatRanking or one method (output from MergeMethods). Each
column is of the same structure as the
slot
ranking of the class GeneRanking. pvals:- The matrix of p-values stored analogously to
rankings. If p-values
have not been computed, this is a matrix of NAs. statistics:- The statistics obtained from altered data sets,
stored analogously to
rankings scheme:- A character for the resampling scheme, can be one
of
"subsampling", "labelexchange",
"bootstrap", "jittering" (if noise
has been added), "merged (rankings)" if several
resampling schemes for the same dataset and ranking method
have been combined via the MergeRankings-method, or
"merged (methods)" if the rankings of several methods have been
combined via the MergeMethods-method.
Methods
- show
- Use
show(RepeatedRanking-Object) for brief information. - toplist
- Use
toplist(RepeatedRanking-Object, k=10)
to get information about the top k=10 genes
for each ranking and one
overview table showing frequencies of gene indices
for each of the ranks 1,...k.
Additionally, only the overview table can be shown with
all other output suppressed using
toplist(RepeatedRanking-Object, show=FALSE). - dispersion
- Genewise variance estimation, s. dispersion,RepeatedRanking-method
- MergeRankings
- Use
MergeRankings(RepeatedRanking-Object1, RepeatedRanking-Object2)
to combine results from different resampling schemes. The
results is again an object of class RepeatedRanking
where the slot scheme is "merged (rankings)" and
all matrices have been concatenated columnwise. - plot
- Use
plot(RepeatedRanking-Object) for a scatterplot
of the reference ranking (slot original) vs. alternative rankings (slot rankings). - HeatmapRankings
- s. HeatmapRankings