runBreakaway: Clonotype richness estimation with Breakaway

In kstreet13/VDJdive: Analysis Tools for 10X V(D)J Data

Clonotype richness estimation with Breakaway

Description

This function uses the Breakaway method to estimate the clonotype richness (total number of clonotypes) present in each group of a clonoStats object.

Usage

runBreakaway(x, ...)

## S4 method for signature 'clonoStats'
runBreakaway(x, nof1 = FALSE, ...)

Arguments

x	A clonoStats object.
...	Additional arguments passed to breakaway or breakaway_nof1.
nof1	logical. Indicates whether to use the breakaway_nof1 function, for abundance data that may contain spurious singletons.

Value

A list of alpha_estimate objects, one per group, containing detailed results of running the Breakaway estimator on the vector of clonotype frequencies from that group.

References

Willis, A. and Bunge, J. (2015). Estimating diversity via frequency ratios. Biometrics.

Willis, A. (2015). Species richness estimation with high diversity but spurious singletons. arXiv.

Examples

data('contigs')
x <- clonoStats(contigs, method = 'unique')
runBreakaway(x)

kstreet13/VDJdive documentation built on May 31, 2024, 1:26 p.m.