topSEA: topSEA

In rSEA: Simultaneous Enrichment Analysis

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 thresholded 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, whcih muct 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}}

rSEA documentation built on March 23, 2020, 5:09 p.m.