makeTSE: A toy TreeSummarizedExperiment object

In fionarhuang/TreeSummarizedExperiment: TreeSummarizedExperiment: a S4 Class for Data with Tree Structures

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()

fionarhuang/TreeSummarizedExperiment documentation built on Aug. 18, 2021, 12:15 p.m.