IFAA
This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see IFAA.
Robust Inference for Absolute Abundance in Microbiome Analysis
Bioconductor version: 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>
citation("IFAA")):
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")| IFAA | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Microbiome, Regression, Sequencing, Software, Technology |
| Version | 1.2.0 |
| 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 |
See More
| Suggests | knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |