trimOnConfounders: Trim based on confounders to avoid taxa with only zero counts

In RCM: Fit row-column association models with the negative binomial distribution for the microbiome

Description

Trim based on confounders to avoid taxa with only zero counts

Usage

trimOnConfounders(confounders, X, prevCutOff, minFraction, n)

Arguments

confounders	a nxt confounder matrix
X	the nxp data matrix
prevCutOff	a scalar between 0 and 1, the prevalence cut off
minFraction	a scalar between 0 and 1, each taxon's total abundance should equal at least the number of samples n times minFraction, otherwise it is trimmed
n	the number of samples Should be called prior to fitting the independence model

Value

A trimmed data matrix nxp'

RCM documentation built on Nov. 8, 2020, 5:22 p.m.