hashSD: 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 OTU numbers.

Usage

hashSD(rare_depth = 0.5, otu_number_range = c(10, 100, 1000, 10000),
  sim_number = 100, sequence_depth = 10)

Arguments

rare_depth	proportion of sequence counts to retain after subsampling
otu_number_range	numeric vector, including the range of numbers of simulated OTUs to test
sim_number	number of simulated subjects per OTU number
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

simSampW, calcDistW

Examples

hashSD(0.5,c(10,100,1000),1000,10)
sapply(hashSD(),FUN=function(x) {sd(lowerTriDM(calcWJstudy(x)))})

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