divLevel: compute diversity indices

In ph-pham/RepSeq: Analysis of High-throughput sequencing repertoire data (RepSeqTools)

Description

function computes diversity indices for level VJ, V or J

Usage

divLevel(
  x,
  index = c("shannon", "simpson", "invsimpson"),
  level = c("VJ", "V", "J"),
  norm = TRUE,
  base = exp(1)
)

Arguments

x	a object of class RepSeqExperiment.
index	diversity index, the choice are "shannon", "simpson", "invsimpson".
level	diversity index should be computed for the level "V", "J", or "VJ".
norm	normalized diversity index will be returned (divided by log(S) with S number of observed species).
base	log base . Default value: exp(1)

Value

a data.table of diversity indices computed at the level "level".

Examples

## Not run: 
# The package RepSeqData contains example datasets 
library(RepSeqData)
divindices <- divLevel(x = RepSeqData, index = "shannon", level = "VJ")
divindices

## End(Not run)

ph-pham/RepSeq documentation built on Dec. 22, 2021, 7:47 a.m.