multimodality {microbiome}R Documentation

Multimodality Score

Description

Multimodality score based on bootstrapped potential analysis.

Usage

multimodality(
  x,
  peak.threshold = 1,
  bw.adjust = 1,
  bs.iter = 100,
  min.density = 1,
  verbose = TRUE
)

Arguments

x

A vector, or data matrix (variables x samples)

peak.threshold

Mode detection threshold

bw.adjust

Bandwidth adjustment

bs.iter

Bootstrap iterations

min.density

minimum accepted density for a maximum; as a multiple of kernel height

verbose

Verbose

Details

Repeats potential analysis (Livina et al. 2010) multiple times with bootstrap sampling for each row of the input data (as in Lahti et al. 2014) and returns the specified results.

Value

A list with following elements:

Author(s)

Leo Lahti leo.lahti@iki.fi

References

Examples

#data(peerj32)
#s <- multimodality(t(peerj32$microbes[, c('Akkermansia', 'Dialister')]))

[Package microbiome version 1.15.1 Index]