hashMean: Simulate a list of OTU tables to create a hash table relating...

In smvargas/PERMANOVA: Power estimation for microbiome studies using pairwise distances and PERMANOVA.

Description

Extends the simSamp function to generate a list of OTU tables representing different levels of subsampling.

Usage

hashMean(rare_levels = runif(1000, 0, 1), rep_per_level = 1,
  otu_number = 1000, sequence_depth = 1)

Arguments

rare_levels	the levels of random subsampling (rarefying), as the proportion of sequence counts to retain after subsampling, to be tested
rep_per_level	number of different levels (proportion of sequence counts to retain after subsampling) tested
otu_number	number of simulated OTUs
sequence_depth	number of sequence counts per OTU bin

Details

For weighted analysis, specify a sequence depth greater than 1; for unweighted analyses, sequence depth is 1 (default).

Value

list of two-dimensional-matrix OTU tables

See Also

simSamp, calcWJstudy

Examples

hashMean(,10,1000,10)
sapply(hashMean(runif(100,0,1),1,1000,10),FUN=function(x) {mean(lowerTriDM(calcWJstudy(x)))})

smvargas/PERMANOVA documentation built on May 20, 2019, 12:37 p.m.