IFAA

DOI: 10.18129/B9.bioc.IFAA  

Robust Inference for Absolute Abundance in Microbiome Analysis

Bioconductor version: Release (3.17)

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>

Installation

To install this package, start R (version "4.3") and enter:

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

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")

 

PDF	R Script	IFAA
PDF		Reference Manual
Text		NEWS

Details

biocViews	Microbiome, Regression, Sequencing, Software, Technology
Version	1.2.0
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
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
LinkingTo
Suggests	knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle
SystemRequirements
Enhances
URL	https://pubmed.ncbi.nlm.nih.gov/35241863/ https://pubmed.ncbi.nlm.nih.gov/30923584/ https://github.com/quranwu/IFAA
BugReports	https://github.com/quranwu/IFAA/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	IFAA_1.2.0.tar.gz
Windows Binary	IFAA_1.2.0.zip
macOS Binary (x86_64)	IFAA_1.2.0.tgz
macOS Binary (arm64)	IFAA_1.2.0.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
Old Source Packages for BioC 3.17	Source Archive