## ---- 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()