Maaslin.wrapper: A wrapper function for MaAsLin

In tvatanen/microbiomics: Microbiomics

Description

This function will run MaAsLin (https://bitbucket.org/biobakery/maaslin/) given a set of taxa and metadata.

This function requires Maaslin-package (https://bitbucket.org/biobakery/maaslin/). However, in order to avoid multiple dependencies this is not explicitely defined as dependency in the microbiomics-package.

Usage

Maaslin.wrapper(taxa, metadata, strOutputDIR = tempfile(),
  variables = colnames(metadata), strRandomCovariates = NULL, ...)

Arguments

taxa	input taxa (samples x taxa data.frame)
metadata	input metadata (samples x features data.frame)
strOutputDIR	output directory (defaults to tmp directory)
variables	subset of metadata columns to test (defaults to all columns)
strRandomCovariates	features to be used as random effects
...	additional parameters for the Maaslin call. Parameters passed to Maaslin.

Value

a list with an association table per feature with associations with taxa.

Author(s)

Tommi Vatanen <[e-mail]>, Raivo Kolde

tvatanen/microbiomics documentation built on Sept. 27, 2019, 7:29 a.m.