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

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

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.