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.
| Version: |
1.1.2 |
| 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 |
| Suggests: |
knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle |
| Published: |
2023-01-12 |
| Author: |
Quran Wu [aut],
Zhigang Li [aut, cre] |
| Maintainer: |
Zhigang Li <lzg2151 at gmail.com> |
| BugReports: |
https://github.com/quranwu/IFAA/issues |
| License: |
GPL-2 |
| URL: |
https://pubmed.ncbi.nlm.nih.gov/35241863/,
https://pubmed.ncbi.nlm.nih.gov/30923584/,
https://github.com/quranwu/IFAA |
| NeedsCompilation: |
no |
| Materials: |
README |
| CRAN checks: |
IFAA results |