## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----echo=FALSE, out.width="90%"---------------------------------------------- knitr::include_graphics("steps.png") ## ----eval=FALSE--------------------------------------------------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("epidecodeR") ## ----setup-------------------------------------------------------------------- library(epidecodeR) ## ----------------------------------------------------------------------------- events<-system.file("extdata", "NOMO-1_ref_peaks.bed", package="epidecodeR") deg<-system.file("extdata", "FTOi.txt", package="epidecodeR") epiobj <- epidecodeR(events = events, deg = deg, pval=0.05, param = 3, ints=c(2,4)) ## ----fig.width=6, fig.height=6------------------------------------------------ makeplot(epiobj, lim = c(-10,10), title = "m6A mediated dysregulation after FTO inhibitor treatment", xlab = "log2FC") ## ----fig.width=6, fig.height=6------------------------------------------------ plot_test(epiobj, title = "m6A mediated dysregulation after FTO inhibitor treatment", ylab = "log2FC") ## ----------------------------------------------------------------------------- events<-system.file("extdata", "eventcounts.txt", package="epidecodeR") events_df<-read.table(events, header = TRUE, row.names = NULL, stringsAsFactors = FALSE, sep = "\t", fill = TRUE) ## ----------------------------------------------------------------------------- head (events_df) ## ----------------------------------------------------------------------------- events<-system.file("extdata", "NOMO-1_ref_peaks.bed", package="epidecodeR") peaks_df<-read.table(events, header = FALSE, row.names = NULL, stringsAsFactors = FALSE, sep = "\t", fill = TRUE) ## ----------------------------------------------------------------------------- head (peaks_df) ## ----------------------------------------------------------------------------- head (get_theoretical_table(epiobj)) ## ----------------------------------------------------------------------------- head (get_empirical_table(epiobj)) ## ----------------------------------------------------------------------------- head (get_grpcounts(epiobj)) ## ----------------------------------------------------------------------------- grptables_list<-get_grptables(epiobj) head (grptables_list$'0') head (grptables_list$'1') head (grptables_list$'2to4') head (grptables_list$'5+') ## ----fig.width=6, fig.height=6------------------------------------------------ makeplot(epiobj, lim = c(-10,10), title = "m6A mediated dysregulation after FTO inhibitor treatment", xlab = "log2FC") ## ----fig.width=6, fig.height=6------------------------------------------------ plot_test(epiobj, title = "m6A mediated dysregulation after FTO inhibitor treatment", ylab = "log2FC") ## ----------------------------------------------------------------------------- sessionInfo()