funBI_harvesting: funBI Harvesting

Description Usage Arguments Value

Description

Perform Harvesting to a list of DIANA hierarcy obetained using the funBI_lot_and_flower function. The available harvesting strategies are three: a delta-threshold strategy, a dynamic strategy with a threshold obtained as a percentage of the total hscore of a considered hierarchical dendrogram, and an automatic strategy using gap statistics.

Usage

1
funBI_harvesting(list_hc, delta, perc, gap, mat, Kmax, B)

Arguments

list_hc

a list of hierarchy resulting from DIANA built from mat

delta

a scalar value indicating the delta-threshold in order to perform a delta-bicluster. In this case perc and gap should be missing.

perc

a scalar value indicated a percentage of the total score in order to perform a delta-bicluster cut using as delta-threshold the percentage perc of the total hscore of a particular dendrogram. In this case delta and gap should be missing.

gap

TRUE/FALSE indicating if gap statistics should be used as Harvesting strategy.In this case delta and perc should be missing.

mat

a matrix

Kmax

the maximum number of clusters to consider when performing gap statistics (gap = TRUE), must be at least two.

B

integer value, number of Monte Carlo (“bootstrap”) samples to consider when performing gap statistics (gap = TRUE).

Value

biclist, a list containing all the candidate biclusters according to the used Harvesting strategy. Every element of the list is a bicluster. Every bicluster is characterized by the following components:

  1. a vector containing the elements belonging to the bicluster reprented using the row index/label of the matrix mat

  2. a vector containing the boundaries of the sub-interval considered represented usign the colum index/label of the matrix mat

  3. the Hscore of the bicluster

  4. The index of list_hc, representing which dendogram the bicluster was cut


JacopoDior/funBI documentation built on May 6, 2019, 12:01 a.m.