## ----'findRegions'-------------------------------------------------------
## Load bumphunter
library('bumphunter')

## Create data from the vignette
pos <- list(pos1=seq(1, 1000, 35),
            pos2=seq(2001, 3000, 35),
            pos3=seq(1, 1000, 50))
chr <- rep(paste0('chr', c(1, 1, 2)), times = sapply(pos, length))
pos <- unlist(pos, use.names = FALSE)

## Find clusters
cl <- clusterMaker(chr, pos, maxGap = 300)

## Build simulated bumps
Indexes <- split(seq_along(cl), cl)
beta1 <- rep(0, length(pos))
for(i in seq(along=Indexes)){
    ind <- Indexes[[i]]
    x <- pos[ind]
    z <- scale(x, median(x), max(x)/12)
    beta1[ind] <- i*(-1)^(i+1)*pmax(1-abs(z)^3,0)^3 ##multiply by i to vary size
}

## Build data
beta0 <- 3 * sin(2 * pi * pos / 720)
X <- cbind(rep(1, 20), rep(c(0, 1), each = 10))
set.seed(23852577)
error <- matrix(rnorm(20 * length(beta1), 0, 1), ncol = 20)
y <- t(X[, 1]) %x% beta0 + t(X[, 2]) %x% beta1 + error

## Perform bumphunting
tab <- bumphunter(y, X, chr, pos, cl, cutoff=.5)

## Explore data
lapply(tab, head)

## ----'buildGRanges'------------------------------------------------------
library('GenomicRanges')

## Build GRanges with sequence lengths
regions <- GRanges(seqnames = tab$table$chr, 
    IRanges(start = tab$table$start, end = tab$table$end),
    strand = '*', value = tab$table$value, area = tab$table$area, 
    cluster = tab$table$cluster, L = tab$table$L, clusterL = tab$table$clusterL)

## Assign chr lengths
data(hg19Ideogram, package = 'biovizBase')
seqlengths(regions) <- seqlengths(hg19Ideogram)[names(seqlengths(regions))]

## Explore the regions
regions

## ----'loadLib'-----------------------------------------------------------
## Load regionReport
library('regionReport')

## ----'createReport'------------------------------------------------------
## Make it so that the report will be available as a vignette
original <- readLines(system.file('regionExploration', 'regionExploration.Rmd',
    package = 'regionReport'))
vignetteInfo <- c(
    'vignette: >',
    '  %\\VignetteEngine{knitr::rmarkdown}',
    '  %\\VignetteIndexEntry{Basic genomic regions exploration}',
    '  %\\VignetteEncoding{UTF-8}'
)
new <- c(original[1:12], vignetteInfo, original[13:length(original)])
writeLines(new, 'regionReportBumphunter.Rmd')

## Now create the report
report <- renderReport(regions, 'Example bumphunter', pvalueVars = NULL,
    densityVars = c('Area' = 'area', 'Value' = 'value',
    'Cluster Length' = 'clusterL'), significantVar = NULL,
    output = 'bumphunterExampleOutput', outdir = '.',
    template = 'regionReportBumphunter.Rmd', device = 'png')
    
## Clean up
file.remove('regionReportBumphunter.Rmd')

## ----'reproducibility'------------------------------------------------------------------------------------------------
## Date generated:
Sys.time()

## Time spent making this page:
proc.time()

## R and packages info:
options(width = 120)
devtools::session_info()

