coda_glmnet_null {coda4microbiome}

coda_glmnet_null

Description

Performs a permutational test for the coda_glmnet() algorithm: It provides the distribution of results under the null hypothesis by implementing the coda_glmnet() on different rearrangements of the response variable.

Usage

coda_glmnet_null(
  x,
  y,
  niter = 100,
  covar = NULL,
  lambda = "lambda.1se",
  alpha = 0.9,
  sig = 0.05
)

Arguments

x

abundance matrix or data frame (rows are samples, columns are variables (taxa))

y

outcome (binary or continuous); data type: numeric, character or factor vector

niter

number of iterations (default = 100)

covar

data frame with covariates (default = NULL)

lambda

penalization parameter (default = "lambda.1se")

alpha

elastic net parameter (default = 0.9)

sig

significance level for the confidence interval (default = 0.05)

Value

a list with "accuracy" and "confidence interval"

Author(s)

M. Calle - T. Susin

Examples

data(Crohn, package = "coda4microbiome")

coda_glmnet_null(x=x_Crohn[,(1:10)], y=y_Crohn, niter=2,covar=NULL,lambda="lambda.1se",
                                                alpha=0.9,sig=0.05)