PALM is a R package and it implements a quasi-Poisson-based framework designed for robust, scalable, and reproducible identification of covariate-associated microbial features in large-scale microbiome association studies and meta-analyses. The package can perform single-study association analysis and meta-analysis across multiple studies.
See following items for more details:
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Article: Wei et al. Fast and reliable association discovery in large-scale microbiome studies and meta-analyses using PALM. Submitted.
Zhoujingpeng Wei @Tang Lab
Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison
The PALM package (version 0.1.0) should be compatible with Windows, Mac, and Linux operating systems.
Before setting up the package, users should have R version 4.3.0 or higher.
The package depends on the following R packages: Mass, dplyr, brglm2 and Rcpp.
Install package from github.
devtools::install_github("ZjpWei/PALM_package")
Install package by source code
install.packages("./PALM_0.1.0.tar.gz", repos = NULL, type = "source")
The following are minimal examples on functionalities of PALM. For more detailes, please refer to its vignette.
- Load package and data
library("PALM")
data("CRC_data", package = "PALM")
CRC_abd <- CRC_data$CRC_abd
CRC_meta <- CRC_data$CRC_meta
########## Generate summary statistics ##########
rel.abd <- list()
covariate.interest <- list()
for(d in unique(CRC_meta$Study)){
rel.abd[[d]] <- CRC_abd[CRC_meta$Sample_ID[CRC_meta$Study == d],]
disease <- as.numeric(CRC_meta$Group[CRC_meta$Study == d] == "CRC")
names(disease) <- CRC_meta$Sample_ID[CRC_meta$Study == d]
covariate.interest[[d]] <- matrix(disease, ncol = 1, dimnames = list(names(disease), "disease"))
}
- Perform meta-analysis
meta.result <- palm(rel.abd = rel.abd, covariate.interest = covariate.interest)
Please use the issues tracker to report any bugs or give any suggestions. Please feel free to contact me Weizhou.
This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License, version 3, as published by the Free Software Foundation.
This program is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU General Public License for more details.
A copy of the GNU General Public License, version 3, is available at https://www.r-project.org/Licenses/GPL-3