filterLowVar: Filter Low Variance Features

In microresearcher/MicroVis: Microbiome Analysis and Visualization

Filter Low Variance Features

Description

Filter Low Variance Features

Usage

filterLowVar(
  dataset = NULL,
  top = NULL,
  var_type = "sd",
  low_var_percentile = NULL,
  silent = F
)

Arguments

dataset	MicroVis dataset (mvdata object)
top	(Optional) Top n number of features to be kept based on relative abundance. Specifying a value for this will override the min_relabun value.
var_type	Method for assessing variance of samples. Current choices are standard deviation ('sd') and interquartile range ('iqr')
low_var_percentile	(Optional) (Default) Variance threshold. Features with variance (standard deviation) lower than this threshold will be filtered out.
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 variance filtering parameters.

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