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.
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numeric a vector of abundances or proportions / frequencies.
character one of the various population calcuations. Choices are: "shannon", "gini", "entropy", "clonality", or "uc50".
pop_calcs Calculations for describing features of populations.
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.
Christopher Nobles, Ph.D.
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