makeTSE {TreeSummarizedExperiment} | R Documentation

## A toy TreeSummarizedExperiment object

### Description

`makeTSE` creates a toy TreeSummarizedExperiment object.

### Usage

    makeTSE(nrow = 10, ncol = 4, include.rowTree = TRUE, include.colTree = TRUE)

### Arguments

`nrow` | a numeric value to specify the number of rows of `TreeSummarizedExperiment`
`ncol` | a numeric value to specify the number of columns of `TreeSummarizedExperiment`
`include.rowTree` | TRUE or FALSE. Default is TRUE, so the output `TreeSummarizedExperiment` has a `phylo` object in `rowTree`.
`include.colTree` | TRUE or FALSE. Default is TRUE, so the output `TreeSummarizedExperiment` has a `phylo` object in `colTree`.

### Details

The `assays` contains a matrix with values from `1:(nrow*ncol)`. The `rowData` has two columns, `var1` and `var2`. `var1` is created with `rep_len(letters, nrow)`. `var2` is created with `rep_len(c(TRUE, FALSE), nrow)`. The `colData` has two columns, `ID` and `group`. `ID` is created with `seq_len(ncol)`. `group` is created with `rep_len(LETTERS[1:2], ncol)`. The row/col tree is generated with `ape::rtree()`. So, to generate reproducible trees, `set.seed()` is required.

### Value

A TreeSummarizedExperiment object

### Author(s)

Ruizhu Huang

### Examples

    set.seed(1)
    makeTSE()

[Package TreeSummarizedExperiment version 2.2.0 Index]