ClusteredScoresList-class: Container for coverage matrices with clustering results.

In markrobinsonuzh/Repitools: Epigenomic tools

Container for coverage matrices with clustering results.

Description

Contains a list of coverage matrices, the parameters that were used to generate them origin, and also cluster membership and expression data.

It also allows the user to take the ScoresList output of featureScores, and do their own custom clustering on the coverage matrices, then save the clustering results in this container.

Constructor

ClusteredScoresList(x, anno = x@anno, scores = tables(x), expr = NULL, expr.name = NULL, cluster.id, sort.name = NULL, sort.data = NULL) Creates a ClusteredScoresList object.

x

A ScoresList object.

anno

A GRanges object. Give this value if only a subset of features was used for clustering.

scores

A list of coverage matrices. Give this if the matrices in x were modified before clustering.

expr

A numeric vector, same length as number of rows of every coverage matrix.

expr.name

A label, describing the expression data.

cluster.id

A vector, same length as number of rows of every coverage matrix.

sort.data

Vector of data to order features within clusters by.

sort.name

Human readable description of what the sorting data is of.

Subsetting

In the following code snippets, x is a ClusteredScoresList object.

x[i] Creates a ClusteredScoresList object, keeping only the i matrices.

subsetRows(x, i = NULL) Creates a ClusteredScoresList object, keeping only the i features.

clusters(x) Creates a ClusteredScoresList object, keeping only the i features.

Accessors

In the following code snippets, x is a ClusteredScoresList object.

clusters(x) Get the cluster ID of each feature.

Author(s)

Dario Strbenac

markrobinsonuzh/Repitools documentation built on March 20, 2024, 6:04 a.m.