topSEA {rSEA}

topSEA

Description

returns a permutation of SEA-chart which rearranges the feature-sets according to the selected argument into ascending or descending order.

Usage

topSEA(object, by, thresh = NULL, descending = TRUE, n = 20, cover)

Arguments

object

A SEA-chart object which is the output of SEA function

by

Variable name by which the ordering should happen. It should be a column of SEA-chart. The default is TDP_bound.

thresh

A real number between 0 and 1. If specified the values of the variable defined in by will be threshold accordingly.

descending

Logical. If TRUE The output chart is organized in a descending order

n

Integer. Number of raws of the output chart

cover

An optional threshold for coverage, which must be a real number between 0 and 1. If specified, feature-sets with a coverage lower than or equal to this value are removed.

Value

Returns a subset of SEA_chart sorted according to the arguments

Author(s)

Mitra Ebrahimpoor

[e-mail]

References

Mitra Ebrahimpoor, Pietro Spitali, Kristina Hettne, Roula Tsonaka, Jelle Goeman, Simultaneous Enrichment Analysis of all Possible Gene-sets: Unifying Self-Contained and Competitive Methods, Briefings in Bioinformatics,bbz074

See Also

SEA

Examples

#See the examples for \code{\link{SEA}}