This package conducts batch effects removal from a taxa read count table by a conditional quantile regression method. The distributional attributes of microbiome data, zero-inflation and over-dispersion, are simultaneously considered. A batch-removed taxa read count table will be generated.
The ConQuR package (version 2.0) should be compatible with Windows, Mac, and Linux operating systems.
Before setting up the package, users should have R version 3.5.0 or higher.
The package depends on the following R packages: quantreg, cqrReg, glmnet, dplyr, doParallel, gplots, vegan, ade4, compositions, randomForest, ROCR, ape, GUniFrac, knitr, rmarkdown, fastDummies.
Users should install doParallel package prior to installing ConQuR (other package dependencies will be taken care during installing ConQuR), from an R terminal:
install.packages("doParallel")
The process should take 3 seconds.
Then, from an R session, install ConQuR by:
devtools::install_github("wdl2459/ConQuR")
The process should take approximately 15 seconds.
To include the vignettes during installing ConQuR, type:
devtools::install_github("wdl2459/ConQuR", build_vignettes = TRUE, force=TRUE)
The process should take approximately 6 minutes.
All functions in ConQuR are described in the manual: https://github.com/wdl2459/ConQuR/blob/main/ConQuR_2.0.pdf
A full analysis based on a sample microbiome data (a random sub-sample of CARDIA data set) is shown in the vignettes, including the standard fitting strategy, penalized fitting strategy, the fine-tuned result, and investigations on the original and batch-removed taxa read count table. The entire analysis should take approximately 6 minutes. Users can find the vignettes at: https://wdl2459.github.io/ConQuR/ConQuR.Vignette.html.
If users include the vignettes during installation, from an R session, type:
browseVignettes("ConQuR")
Due to technical issues, always library doParallel together with ConQuR, from an R session:
library(ConQuR)
library(doParallel)
For detailed use, refer to the materials in Demo.