sparcc: sparcc wrapper

In SOHPIE: Statistical Approach via Pseudo-Value Information and Estimation

sparcc wrapper

Description

SpiecEasi R package, says in his package that this is "a reimplementation of SparCC algorithm (Friedman et Alm, PLoS Comp Bio, 2012)." Installation of SpiecEasi can sometimes generate errors, so I have included Dr. Huaying Fang's sparcc wrapper as one of the functions in this package for the estimation of co-abundance networks. His code was acquired from CCLasso (Fang et al, Bioinformatics, 2015), provided in GitHub (https://github.com/huayingfang/CCLasso).

Usage

sparcc(x, imax = 20, kmax = 10, alpha = 0.1, Vmin = 1e-04)

Arguments

x	count data matrix (OTU table)
imax	Number of iterations in the outer loop
kmax	max iteration steps for SparCC
alpha	threshold for strong correlation
Vmin	absolute value of correlations below this threshold are considered zero by the inner SparCC loop.

Value

This will estimate an association matrix (network) for observed OTU table.

SOHPIE documentation built on Oct. 24, 2023, 1:06 a.m.