| sparcc {SOHPIE} | R Documentation |
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.