# calculateDiversity: Sample diversity estimation In kstreet13/VDJdive: Analysis Tools for 10X V(D)J Data

 calculateDiversity R Documentation

## Sample diversity estimation

### Description

This function uses various methods to estimate the clonotypic diversity of samples based on a matrix of clonotype abundances (samples are columns).

### Usage

``````calculateDiversity(x, ...)

## S4 method for signature 'clonoStats'
calculateDiversity(
x,
methods = c("all", "nCells", "nClonotypes", "shannon", "normentropy", "invsimpson",
"ginisimpson", "chao1", "chaobunge"),
...
)

## S4 method for signature 'SingleCellExperiment'
calculateDiversity(x, ...)
``````

### Arguments

 `x` A matrix of abundance values where rows are features (clonotypes) and columns are samples. This is created with `summarizeClonotypes` using a sparse matrix computed with either `EMquant` or `CRquant`. `...` Additional arguments passed to external calculation methods. `methods` A character vector specifying which diversity measures to use (default = `'all'`, see Details).

### Details

Available methods are total cells with appropriate TCR data (`'nCells'`, not a diversity measure, but a useful point of comparison), total clonotypes (`'nClonotypes'`), Shannon entropy (`'shannon'`), Simpson index (`'simpson'`), inverse Simpson index (`'invsimpson'`), Chao1 richness (`'chao1'`), and Chao-Bunge richness (`'chaobunge'`). A special value of `'all'` is also allowed, which will run all methods listed above.

The `'chao1'` and `'chaobunge'` estimates assume all abundances are integers. When this is not the case for the input matrix, `k`, all values are multiplied by the `scaling_factor` and rounded to the nearest integer. The resulting estimate is then divided by `scaling_factor` to return to the original scale. The `'shannon'`, `'simpson'`, and `'invsimpson'` methods work with any input type.

### Value

A matrix of diversity estimates for each sample. Note that the `'chaobunge'` method also includes an estimate of the standard error.

### Examples

``````data('contigs')
x <- clonoStats(contigs)
calculateDiversity(x)

``````

kstreet13/VDJdive documentation built on May 31, 2024, 1:26 p.m.