filterLowPrev: Filter Low Prevalence Features

In microresearcher/MicroVis: Microbiome Analysis and Visualization

Filter Low Prevalence Features

Description

Filter Low Prevalence Features

Usage

filterLowPrev(
  dataset = NULL,
  top = NULL,
  min_prevalence = NULL,
  prev_prop = NULL,
  silent = F
)

Arguments

dataset	MicroVis dataset (mvdata object)
top	(Optional) Top n number of features to be kept based on prevalence. Specifying a value for this will override the min_prevalence value.
min_prevalence	(Optional) (Default) Prevalence threshold. Features with prevalence lower than this threshold will be filtered out.
prev_prop	(Optional) Minimum percent of samples that a feature must be be present in for it to be kept. Overrides top and min_prevalence values
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 prevalence filtering parameters.

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