aphylo-index: Indexing aphylo objects

In USCbiostats/phylogenetic: Statistical Inference and Prediction of Annotations in Phylogenetic Trees

Indexing aphylo objects

Description

Indexing aphylo objects

Usage

## S3 method for class 'aphylo'
x[i, j, drop = FALSE]

## S3 replacement method for class 'aphylo'
x[i, j] <- value

Arguments

x	An object of class aphylo.
i, j	Integer vector. Indices of genes or functions.
drop	Logical scalar. When TRUE, the function returns a matrix of annotations. Otherwise an object of class aphylo.
value	Integer vector. Replacing values, can be either c(0, 1, 9, NA).

Details

The subsetting method allows selecting one or more annotations from the aphylo object. Whenever i is specified, then aphylo returns the corresponding annotations.

Value

• When indexing with i: A data frame with the annotations of the selected genes.

• When only indexing with j (drop = FALSE): An aphylo object with the selected sets of annotations.

• When only indexing with j (drop = TRUE): A data.frame with the selected annotations.

• When indexing on both i and j: A data.frame with the selected genes and annotations.

Examples

set.seed(12312)
atree <- raphylo(50, P = 4)
atree[1:10,]
atree[,2:3]
atree[, 2:3, drop = TRUE]
atree[1:10, 2:3]

USCbiostats/phylogenetic documentation built on Oct. 28, 2023, 7:23 a.m.