## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----setup-------------------------------------------------------------------- library(RolDE) library(printr) library(knitr) ## ----install RolDE, eval=FALSE, message=FALSE, warning=FALSE------------------ # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager", repos = "http://cran.us.r-project.org") # BiocManager::install("RolDE") ## ----load data1, echo=TRUE---------------------------------------------------- data(data1) data("des_matrix1") ## ----explore data1, echo=TRUE------------------------------------------------- dim(data1) ## ----explore data1 2, echo=TRUE----------------------------------------------- head(colnames(data1)) ## ----explore data1 3, echo=TRUE----------------------------------------------- dim(des_matrix1) ## ----explore data1 4, echo=TRUE----------------------------------------------- colnames(des_matrix1) ## ----explore data1 5, echo=TRUE----------------------------------------------- head(des_matrix1) tail(des_matrix1) ## ----explore data1 6, echo=TRUE----------------------------------------------- unique(des_matrix1[,1]) ## ----explore data1 7, echo=TRUE----------------------------------------------- unique(des_matrix1[,2]) table(des_matrix1[,2]) ## ----explore data1 8, echo=TRUE----------------------------------------------- unique(des_matrix1[,3]) table(des_matrix1[,3]) ## ----explore data1 9, echo=TRUE----------------------------------------------- unique(des_matrix1[,4]) table(des_matrix1[,4]) ## ----RolDE data1, echo=TRUE, eval=FALSE--------------------------------------- # set.seed(1) # data1.res<-RolDE(data=data1, des_matrix=des_matrix1, n_cores=3) ## ----RolDE SE usage, echo=TRUE, eval=FALSE------------------------------------ # SE_object_for_RolDE = SummarizedExperiment(assays=list(data1), # colData = des_matrix1) ## ----RolDE SE object run, echo=TRUE, eval=FALSE------------------------------- # set.seed(1) # data1.res<-RolDE(data=SE_object_for_RolDE, n_cores=3) ## ----explore RolDE res data1, echo=FALSE-------------------------------------- data(res1) data1.res=res1 ## ----explore RolDE res data1 2, echo=TRUE------------------------------------- names(data1.res) ## ----explore RolDE res data1 3, echo=TRUE------------------------------------- RolDE.data1<-data1.res$RolDE_Results dim(RolDE.data1) colnames(RolDE.data1) ## ----explore RolDE res data1 4, echo=TRUE, fig.height=5, fig.width=7---------- RolDE.data1<-RolDE.data1[order(as.numeric(RolDE.data1[,2])),] head(RolDE.data1, 5) ## ----explore RolDE res data1 5, echo=TRUE, fig.height=5, fig.width=7---------- hist(RolDE.data1$`Estimated Significance Value`, main = "Estimated significance values", xlab="") ## ----explore RolDE res data1 6, echo=TRUE------------------------------------- length(which(RolDE.data1$`Adjusted Estimated Significance Value`<=0.05)) ## ----explore data3, echo=TRUE------------------------------------------------- data("data3") data("des_matrix3") ?data3 ## ----Run RolDE for data3, echo=TRUE, eval=FALSE------------------------------- # set.seed(1) # data3.res<-RolDE(data=data3, des_matrix=des_matrix3, n_cores=3, sig_adj_meth = "bonferroni") ## ----explore RolDE res data3, echo=FALSE-------------------------------------- data(res3) data3.res=res3 ## ----explore RolDE res data3 2, echo=TRUE, fig.height=5, fig.width=7---------- RolDE.data3<-data3.res$RolDE_Results RolDE.data3<-RolDE.data3[order(as.numeric(RolDE.data3[,2])),] head(RolDE.data3, 3) ## ----explore RolDE res data3 3, echo=TRUE, fig.height=5, fig.width=7---------- hist(RolDE.data3$`Estimated Significance Value`, main = "Estimated significance values", xlab="") ## ----explore RolDE res data3 4, echo=TRUE, fig.height=5, fig.width=7---------- grep("ups", RolDE.data3[,1]) ## ----explore RolDE res data3 5, echo=TRUE, fig.height=5, fig.width=7---------- length(which(RolDE.data3[,4]<=0.05)) ## ----plotfindings, echo=TRUE, fig.height=5, fig.width=7----------------------- ?plotFindings ## ----change RolDE parameters, echo=TRUE, eval=FALSE--------------------------- # set.seed(1) # data1.res<-RolDE(data=data1, des_matrix=des_matrix1, doPar=T, n_cores=3, min_comm_diff = c(4,3)) ## ----change RolDE parameters 2, echo=TRUE, eval=FALSE------------------------- # set.seed(1) # data1.res<-RolDE_Main(data=data1, des_matrix=des_matrix1, n_cores=3, degree_RegROTS = 2, degree_PolyReg = 3) ## ----change RolDE parameters 3, echo=TRUE, eval=FALSE------------------------- # set.seed(1) # data1.res<-RolDE_Main(data=data1, des_matrix=des_matrix1, n_cores=3, model_type="mixed0") ## ----change RolDE parameters 4, echo=TRUE, eval=FALSE------------------------- # set.seed(1) # data1.res<-RolDE(data=data1, des_matrix=des_matrix1, n_cores=3, model_type="mixed1") ## ----session info, echo=TRUE-------------------------------------------------- #Session info sessionInfo()