pop_calcs: Calculation for descriptors of populations

Description Usage Arguments Details Functions Author(s) Examples

View source: R/pop_calcs.R

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

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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

Author(s)

Christopher Nobles, Ph.D.

Examples

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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.