runSampleFilter: Sample Filter

In microresearcher/MicroVis: Microbiome Analysis and Visualization

Sample Filter

Description

This function is one of the processing functions called by processDataset() removes samples from low quality samples identified by removeLowQuality(), groups excluded by chooseGrps()/addGrps()/removeGrps() , and samples specifically excluded by removeSamples()

Usage

runSampleFilter(dataset = NULL, temp = F, silent = F)

Arguments

dataset	MicroVis dataset (mvdata object)
temp	This parameter has no use in this function and can be removed
silent	Argument that is ultimately passed onto runSampleFilter(), runFeatureFilter(), and runNormalizer(). If TRUE, it tells these functions to NOT print out any of their processing messages.

Value

MicroVis dataset (mvdata object) with the following samples removed: 1) Low quality samples identified by removeLowQuality() 2) Samples in groups excluded by chooseGrps()/addGrps()/removeGrps() 3) Specific samples removed by the user using removeSamples()

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