ClusteredScoresList {Repitools} | R Documentation

## 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

[Package Repitools version 1.30.0 Index]