sparcc wrapper

**
Description
A reimplementation of SparCC algorithm (Friedman et Alm 2012, PLoS Comp Bio, 2012).

Usage
sparcc(data, iter = 20, inner_iter = 10, th = 0.1)
Arguments
data Community count data matrix

iter Number of iterations in the outer loop

inner_iter Number of iterations in the inner loop

th absolute value of correlations below this threshold are considered zero by the inner SparCC loop.

Bootstrap SparCC

Description
Get bootstrapped estimates of SparCC correlation coefficients. To get empirical p-values, pass this output to pval.sparccboot.

Usage
sparccboot(
data,
sparcc.params = list(),
statisticboot = function(data, indices) triu(do.call(“sparcc”, c(list(data[indices, ,
drop = FALSE]), sparcc.params))$Cor),statisticperm=function(data,indices)triu(do.call("sparcc",c(list(apply(data[indices,],2,sample)),sparcc.params))$Cor),
R,
ncpus = 1,
…
)
Arguments
data Community count data

sparcc.params named list of parameters to pass to sparcc

statisticboot function which takes data and bootstrap sample indices and results the upper triangle of the bootstapped correlation matrix

statisticperm function which takes data and permutated sample indices and results the upper triangle of the null correlation matrix

R number of bootstraps

ncpus number of cores to use for parallelization

…
additional arguments that are passed to boot::boot