# pop_calcs: Calculation for descriptors of populations In cnobles/gintools: Genomic DNA Integration Analysis Tools

## Description

Given a population of integration sites, TCR/IGH sequences, etc., a numerical value can be used to describe the diveristy (shannon index or entropy), or the clonality (gini or clonality). These numerical values allow for a comparison to be made between populations. Entropy and Clonality are factors used by Adaptive Biotechnologies to describe their TCR / IGH sequence data.

## Usage

 ``` 1 2 3 4 5 6 7 8 9 10 11``` ```pop_calcs(x, calc) calc_shannon(x, base = exp(1)) calc_gini(x, wt = NULL) calc_entropy(x) calc_clonality(x) calc_uc50(x) ```

## Arguments

 `x` numeric a vector of abundances or proportions / frequencies. `calc` character one of the various population calcuations. Choices are: "shannon", "gini", "entropy", "clonality", or "uc50".

## Details

`pop_calcs` Calculations for describing features of populations.

## Functions

• `calc_shannon`: Calculate Shannon Diversity.

• `calc_gini`: Calculate gini index.

• `calc_entropy`: Calculate Entropy as defined by Adaptive Biotech.

• `calc_clonality`: Calcuate Clonality as defined by Adaptive Biotech.

• `calc_uc50`: Calculate UC50 or the number of must abundant clones which make up half the population.

## Author(s)

Christopher Nobles, Ph.D.

## Examples

 ```1 2 3 4 5 6 7``` ```x <- sample(1:100, 50, replace = TRUE) pop_calcs(x, calc = "shannon") pop_calcs(x, calc = "gini") pop_calcs(x, calc = "entropy") pop_calcs(x, calc = "clonality") pop_calcs(x, calc = "uc50") ```

cnobles/gintools documentation built on Aug. 22, 2019, 10:36 a.m.