simPower: Simulate a list of OTU tables encoding a range of effect...

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

Description

Extends the simStudy function to generate a list of OTU tables according to a specified range of group-level effects.

Usage

simPower(group_size_vector = c(100, 100, 100), otu_number = 1000,
  sequence_depth = 1, rare_depth = 0.5, effect_range = seq(0, 0.3,
  length.out = 100))

Arguments

group_size_vector	numeric vector representing subjects per exposure/intervention group
otu_number	number of simulated OTUs
sequence_depth	number of sequence counts per OTU bin
rare_depth	proportion of sequence counts to retain after subsampling
effect_range	range of proportions of unique community membership in affected group of subjects

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, with row and column names to suit downstream analysis

See Also

simStudy, calcUJstudy, calcWJstudy

Examples

simPower(c(16,16,16),100,10,0.8,seq(0,0.3,length.out=100))
sapply(simPower(c(16,16,16),100,10,0.8,seq(0,0.3,length.out=100)),FUN=function(x) {calcOmega2(calcWJstudy(x))})

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