HMP (version 2.0.1)

Test.Paired: Test Paired Data Sets

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

# NOT RUN {
	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
# }