bioc-issue-bot
commented
1 year ago Hi @EvaYiwenWang
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: PLSDAbatch
Type: Package
Title: PLSDA-batch
Version: 0.99.0
Authors@R:
c(person(given = "Yiwen", family = "Wang", middle = "(Eva)", role = c("aut", "cre"), email = "anjiwangyiwen@gmail.com", comment=c(ORCID="0000-0002-7067-9093")),
person(given = "Kim-Anh", family = "Le Cao", role = "aut", email = "kimanh.lecao@unimelb.edu.au"))
Description: A novel framework to correct for batch effects prior to any downstream analysis in microbiome data based on Projection to Latent Structures Discriminant Analysis. The main method is named “PLSDA-batch”. It first estimates treatment and batch variation with latent components, then subtracts batch-associated components from the data whilst preserving biological variation of interest. PLSDA-batch is highly suitable for microbiome data as it is non-parametric, multivariate and allows for ordination and data visualisation. Combined with centered log-ratio transformation for addressing uneven library sizes and compositional structure, PLSDA-batch addresses all characteristics of microbiome data that existing correction methods have ignored so far. Two other variants are proposed for 1/ unbalanced batch x treatment designs that are commonly encountered in studies with small sample sizes, and for 2/ selection of discriminative variables amongst treatment groups to avoid overfitting in classification problems. These two variants have widened the scope of applicability of PLSDA-batch to different data settings.
License: GPL-3
Depends:
R (>= 4.3.0)
Imports:
mixOmics,
scales,
Rdpack,
ggplot2,
gridExtra,
ggpubr,
lmerTest,
performance,
grid,
stats
Suggests:
BiocStyle,
knitr,
rmarkdown,
vegan,
testthat,
Biobase,
badger
biocViews:
StatisticalMethod,
DimensionReduction,
PrincipalComponent,
Classification,
Microbiome,
BatchEffect,
Normalization,
Visualization
VignetteBuilder: knitr
RdMacros: Rdpack
RoxygenNote: 7.2.3
Encoding: UTF-8
BugReports: https://github.com/EvaYiwenWang/PLSDAbatch/issues/
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