Description Usage Arguments Details Functions Author(s) Examples
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.
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)

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". 
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.
1 2 3 4 5 6 7 
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