This vignette describes the use of DEHOGT, a package for identifying differentially expressed genes using a generalized linear model approach. The package supports quasi-Poisson and negative binomial models to accommodate overdispersion in gene expression count data, integrating factors such as treatment effects, normalization, and significance testing.
DEHOGT 0.99.0
DEHOGT is designed to handle overdispersion in count data using a generalized linear model (GLM) framework. The package supports quasi-Poisson and negative binomial models, making it useful for differential expression analysis of RNA-seq and other count-based data types.
if (!require("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("DEHOGT")In this example, we simulate gene expression data and perform differential expression analysis using the quasi-Poisson model. We also show how to incorporate covariates and normalization factors.
## Simulate gene expression data (100 genes, 10 samples)
data <- matrix(rpois(1000, 10), nrow = 100, ncol = 10)
## Randomly assign treatment groups
treatment <- sample(0:1, 10, replace = TRUE)
## Load DEHOGT package
library(DEHOGT)
## Run the function with 2 CPU cores
result <- dehogt_func(data, treatment, num_cores = 2)
## Display results
head(result$pvals)## [1] 0.61975487 0.64322312 0.07246888 0.25653401 0.56751532 0.68997976# Example: Adding covariates and normalization factors
covariates <- matrix(rnorm(1000), nrow = 100, ncol = 10)
norm_factors <- rep(1, 10)
# Run with covariates and normalization factors
result_cov <- dehogt_func(data, treatment, covariates = covariates, norm_factors = norm_factors, num_cores = 2)sessionInfo()R version 4.4.1 (2024-06-14) Platform: aarch64-apple-darwin20 Running under: macOS Sonoma 14.6.1
Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale: [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Los_Angeles tzcode source: internal
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] DEHOGT_0.99.0 BiocStyle_2.32.1
loaded via a namespace (and not attached):
[1] digest_0.6.37 R6_2.5.1 codetools_0.2-20
[4] bookdown_0.40 fastmap_1.2.0 doParallel_1.0.17
[7] xfun_0.47 iterators_1.0.14 cachem_1.1.0
[10] parallel_4.4.1 knitr_1.48 htmltools_0.5.8.1
[13] rmarkdown_2.28 lifecycle_1.0.4 cli_3.6.3
[16] foreach_1.5.2 sass_0.4.9 jquerylib_0.1.4
[19] compiler_4.4.1 tools_4.4.1 evaluate_0.24.0
[22] bslib_0.8.0 yaml_2.3.10 BiocManager_1.30.25
[25] jsonlite_1.8.8 rlang_1.1.4 MASS_7.3-61