Test.Paired: Test Paired Data Sets

In HMP: Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP

Description

Tests two paired data sets for similarity.

Usage

Test.Paired(group.data, numPerms = 1000, parallel = FALSE, cores = 3)

Arguments

group.data	A list of 2 matrices of taxonomic counts(columns) for each sample(rows).
numPerms	Number of permutations. In practice this should be at least 1,000.
parallel	When this is 'TRUE' it allows for parallel calculation of the permutations. Requires the package doParallel.
cores	The number of parallel processes to run if parallel is 'TRUE'.

Value

A pvalue.

Examples

	data(saliva)
	data(throat)
	
	
	### Since saliva and throat come from same subjects, the data is paired 
	saliva1 <- saliva[-24,] # Make saliva 23 subjects to match throat
	group.data <- list(throat, saliva1)
	
	### We use 1 for speed, should be at least 1,000
	numPerms <- 1
	
	pval <- Test.Paired(group.data, numPerms)
	pval

Example output

Loading required package: dirmult

Attaching package: 'HMP'

The following object is masked from 'package:dirmult':

    weirMoM

[1] 0.5

HMP documentation built on Aug. 31, 2019, 5:05 p.m.