## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE, warning = FALSE, message = FALSE, fig.retina = 2, dpi = 96, fig.width = 7.2916667, fig.asp = 0.6178571) ## ----simulated_data----------------------------------------------------------- library("CytoGLMM") library("magrittr") set.seed(23) df = generate_data() df[1:5,1:5] ## ----protein_names------------------------------------------------------------ protein_names = names(df)[3:12] ## ----transform---------------------------------------------------------------- df %<>% dplyr::mutate_at(protein_names, function(x) asinh(x/5)) ## ----glm_fit------------------------------------------------------------------ glm_fit = CytoGLMM::cytoglm(df, protein_names = protein_names, condition = "condition", group = "donor", num_cores = 1, num_boot = 1000) glm_fit ## ----glm_plot----------------------------------------------------------------- plot(glm_fit) ## ----glm_summarize------------------------------------------------------------ summary(glm_fit) ## ----glm_p_values------------------------------------------------------------- summary(glm_fit) %>% dplyr::filter(pvalues_adj < 0.05) ## ----glmm_fit----------------------------------------------------------------- glmm_fit = CytoGLMM::cytoglmm(df, protein_names = protein_names, condition = "condition", group = "donor", num_cores = 1) glmm_fit ## ----glmm_plot---------------------------------------------------------------- plot(glmm_fit) ## ----glmm_summarize----------------------------------------------------------- summary(glmm_fit) ## ----glmm_p_values------------------------------------------------------------ summary(glmm_fit) %>% dplyr::filter(pvalues_adj < 0.05) ## ----session_info------------------------------------------------------------- sessionInfo()