filterLowAbun: Filter Low Abundance Features

In microresearcher/MicroVis: Microbiome Analysis and Visualization

Filter Low Abundance Features

Description

Filter Low Abundance Features

Usage

filterLowAbun(
  dataset = NULL,
  min_abun = NULL,
  min_proportion = NULL,
  silent = F
)

Arguments

dataset	MicroVis dataset (mvdata object)
min_abun	(Optional) (Default = 1) Abundance threshold. Only features with at least this much abundance in min_proportion percent of samples will be KEPT.
min_proportion	(Optional) (Default = 20) Low abundance proportion threshold. Only features with at least min_abun abundance in this percentage of samples will be KEPT.
silent	Argument that is ultimately passed onto runSampleFilter(), runNormalization(), and runFeatureFilter(), telling them not to output any messages.

Value

MicroVis dataset (mvdata object) with updated low abundance filtering parameters.

microresearcher/MicroVis documentation built on Feb. 8, 2024, 10:59 a.m.