## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE)

## ----eval = FALSE-------------------------------------------------------------
#  BiocManager::install("TADCompare")

## ----echo = FALSE, warning = FALSE, message=FALSE-----------------------------
library(dplyr)
library(TADCompare)

## ----warning=FALSE, message = FALSE, eval=FALSE-------------------------------
#  library(rGREAT)
#  # Reading in data
#  data("rao_chr22_prim")
#  data("rao_chr22_rep")
#  
#  # Performing differential analysis
#  results <- TADCompare(rao_chr22_prim, rao_chr22_rep, resolution = 50000)
#  
#  # Saving the results into its own data frame
#  TAD_Frame <- results$TAD_Frame
#  
#  # Filter data to only include complex boundaries enriched in the second
#  # contact matrix
#  TAD_Frame <- TAD_Frame %>% dplyr::filter((Type == "Shifted") &
#                                           (Enriched_In == "Matrix 2"))
#  
#  # Assign a chromosome and convert to a bed format
#  TAD_Frame <- TAD_Frame %>% dplyr::select(Boundary) %>% mutate(chr = "chr22",
#      start = Boundary, end = Boundary) %>% dplyr::select(chr, start, end)
#  
#  # Set up rGREAT job with default parameters
#  great_shift <- submitGreatJob(TAD_Frame, request_interval = 1, version = "2.0")
#  
#  # Submit the job
#  enrichment_table <- getEnrichmentTables(great_shift)
#  
#  # Subset to only include vital information
#  enrichment_table <- bind_rows(enrichment_table, .id = "source") %>%
#    dplyr::select(Ontology = source, Description = name,
#                  `P-value` = Hyper_Raw_PValue)
#  
#  # Print head organizaed by p-values
#  head(enrichment_table %>% dplyr::arrange(`P-value`))

## ----warning=FALSE, message = FALSE, eval=FALSE-------------------------------
#  # Read in time course data
#  data("time_mats")
#  # Identifying boundaries
#  results <- TimeCompare(time_mats, resolution = 50000)
#  
#  # Pulling out the frame of TADs
#  TAD_Frame <- results$TAD_Bounds
#  
#  # Getting coordinates for TAD boundaries and converting into bed format
#  Bound_List <- lapply(unique(TAD_Frame$Category), function(x) {
#      TAD_Frame %>% filter((Category == x)) %>% mutate(chr = "chr22") %>%
#          dplyr::select(chr, Coordinate) %>%
#          mutate(start = Coordinate, end = Coordinate) %>%
#          dplyr::select(chr, start, end)
#  })
#  
#  # Performing rGREAT analysis for each boundary Category
#  TAD_Enrich <- lapply(Bound_List, function(x) {
#    getEnrichmentTables(submitGreatJob(x, request_interval = 1, version = "2.0"))
#  })
#  
#  # Name list of data frames to keep track of which enrichment belongs to which
#  names(TAD_Enrich) <- unique(TAD_Frame$Category)
#  
#  # Bind each category of pathway and create new column for each pathway
#  TAD_Enrich <- lapply(names(TAD_Enrich), function(x) {
#    bind_rows(lapply(TAD_Enrich[[x]], function(y) {
#      y %>% mutate(Category = x)
#    }), .id = "source")
#  })
#  
#  # Bind each boundary category together and pull out important variables
#  enrichment_table <- bind_rows(TAD_Enrich) %>%
#    dplyr::select(Ontology = source, Description = name,
#                  `P-value` = Hyper_Raw_PValue, Category)
#  
#  # Get the top enriched pathways
#  head(enrichment_table %>% dplyr::arrange(`P-value`))

## -----------------------------------------------------------------------------
sessionInfo()