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IFAA

This is the development version of IFAA; for the stable release version, see IFAA.

Robust Inference for Absolute Abundance in Microbiome Analysis


Bioconductor version: Development (3.19)

This package offers a robust approach to make inference on the association of covariates with the absolute abundance (AA) of microbiome in an ecosystem. It can be also directly applied to relative abundance (RA) data to make inference on AA because the ratio of two RA is equal to the ratio of their AA. This algorithm can estimate and test the associations of interest while adjusting for potential confounders. The estimates of this method have easy interpretation like a typical regression analysis. High-dimensional covariates are handled with regularization and it is implemented by parallel computing. False discovery rate is automatically controlled by this approach. Zeros do not need to be imputed by a positive value for the analysis. The IFAA package also offers the 'MZILN' function for estimating and testing associations of abundance ratios with covariates.

Author: Quran Wu [aut], Zhigang Li [aut, cre]

Maintainer: Zhigang Li <lzg2151 at gmail.com>

Citation (from within R, enter citation("IFAA")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("IFAA")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("IFAA")
IFAA PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Microbiome, Regression, Sequencing, Software, Technology
Version 1.5.2
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License GPL-2
Depends R (>= 4.2.0)
Imports mathjaxr, doRNG, foreach (>= 1.4.3), Matrix (>= 1.4-0), HDCI (>= 1.0-2), parallel (>= 3.3.0), doParallel (>= 1.0.11), parallelly, glmnet, stats, utils, SummarizedExperiment, stringr, S4Vectors, DescTools, MatrixExtra, methods
System Requirements
URL https://pubmed.ncbi.nlm.nih.gov/35241863/ https://pubmed.ncbi.nlm.nih.gov/30923584/ https://github.com/quranwu/IFAA
Bug Reports https://github.com/quranwu/IFAA/issues
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Suggests knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package IFAA_1.5.2.tar.gz
Windows Binary IFAA_1.5.2.zip
macOS Binary (x86_64) IFAA_1.5.2.tgz
macOS Binary (arm64) IFAA_1.5.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/IFAA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/IFAA
Bioc Package Browser https://code.bioconductor.org/browse/IFAA/
Package Short Url https://bioconductor.org/packages/IFAA/
Package Downloads Report Download Stats