enve.prefscore: Enveomics: Pref Score

In enveomics.R: Various Utilities for Microbial Genomics and Metagenomics

Enveomics: Pref Score

Description

Estimate preference score of species based on occupancy in biased sample sets

Usage

enve.prefscore(
  x,
  set,
  ignore = NULL,
  signif.thr,
  plot = TRUE,
  col.above = rgb(148, 17, 0, maxColorValue = 255),
  col.equal = rgb(189, 189, 189, maxColorValue = 255),
  col.below = rgb(47, 84, 150, maxColorValue = 255),
  ...
)

Arguments

x	Occupancy matrix (logical or numeric binary) with species as rows and samples as columns
set	Vector indicating samples in the test set. It can be any selection vector: boolean (same length as the number of columns in x), or numeric or character vector with indexes of the x columns.
ignore	Vector indicating species to ignore. It can be any selection vector with respect to the rows in x (see set).
signif.thr	Absolute value of the significance threshold
plot	Indicates if a plot should be generated
col.above	Color for points significantly above zero
col.equal	Color for points not significantly different from zero
col.below	Color for points significantly below zero
...	Any additional parameters supported by plot

Value

Returns a named vector of preference scores.

Author(s)

Luis M. Rodriguez-R [aut, cre]

enveomics.R documentation built on April 3, 2025, 9:06 p.m.