## -----------------------------------------------------------------------------
library(chipenrich)

## ----warning = FALSE, message = FALSE-----------------------------------------
data(peaks_E2F4, package = 'chipenrich.data')
data(peaks_H3K4me3_GM12878, package = 'chipenrich.data')

head(peaks_E2F4)
head(peaks_H3K4me3_GM12878)

## -----------------------------------------------------------------------------
supported_genomes()

## -----------------------------------------------------------------------------
# Take head because it's long
head(supported_locusdefs())

## ----eval=FALSE---------------------------------------------------------------
#  chr	start	end	geneid
#  chr1	839460	839610	148398
#  chr1	840040	840190	148398
#  chr1	840040	840190	57801
#  chr1	840800	840950	148398
#  chr1	841160	841310	148398

## -----------------------------------------------------------------------------
# Take head because it's long
head(supported_genesets())

## ----eval=FALSE---------------------------------------------------------------
#  gs_id	gene_id
#  GO:0006631	30
#  GO:0006631	31
#  GO:0006631	32
#  GO:0006631	33
#  GO:0006631	34
#  GO:0006631	35
#  GO:0006631	36
#  GO:0006631	37
#  GO:0006631	51
#  GO:0006631	131
#  GO:0006631	183
#  GO:0006631	207
#  GO:0006631	208
#  GO:0006631	215
#  GO:0006631	225

## ----eval = F-----------------------------------------------------------------
#  library(EGSEAdata)
#  egsea.data("mouse")
#  temp = Mm.H #Or some other gene sets
#  geneset = do.call(rbind,lapply(1:length(temp), function(index) {data.frame(gs_id = rep(names(temp)[index], length(temp[[index]])),gene_id = unlist(strsplit(temp[[index]],split = " ")),stringsAsFactors = F)}))
#  write.table(geneset, "./custom_geneset.txt", quote=F, sep="\t",row.names = F, col.names = T)

## -----------------------------------------------------------------------------
# Take head because it's long
head(supported_read_lengths())

## ----eval=FALSE---------------------------------------------------------------
#  mappa	gene_id
#  0.8	8487
#  0.1	84
#  0.6	91
#  1	1000

## ----warning = FALSE, message = FALSE-----------------------------------------
gs_path = system.file('extdata','vignette_genesets.txt', package='chipenrich')
results = broadenrich(peaks = peaks_H3K4me3_GM12878, genome = 'hg19', genesets = gs_path, locusdef = "nearest_tss", qc_plots = FALSE, out_name = NULL, n_cores=1)
results.be = results$results
print(results.be[1:5,1:5])

## ----warning = FALSE, message = FALSE-----------------------------------------
# Without mappability
gs_path = system.file('extdata','vignette_genesets.txt', package='chipenrich')
results = chipenrich(peaks = peaks_E2F4, genome = 'hg19', genesets = gs_path,locusdef = "nearest_tss", qc_plots = FALSE, out_name = NULL, n_cores = 1)
results.ce = results$results
print(results.ce[1:5,1:5])

## ----warning = FALSE, message = FALSE-----------------------------------------
# With mappability
gs_path = system.file('extdata','vignette_genesets.txt', package='chipenrich')
results = chipenrich(peaks = peaks_E2F4, genome = 'hg19', genesets = gs_path, locusdef = "nearest_tss", mappability=24, qc_plots = FALSE,out_name = NULL,n_cores=1)
results.cem = results$results
print(results.cem[1:5,1:5])

## ----warning = FALSE, message = FALSE-----------------------------------------
gs_path = system.file('extdata','vignette_genesets.txt', package='chipenrich')
results = polyenrich(peaks = peaks_E2F4, genome = 'hg19', genesets = gs_path, method = 'polyenrich', locusdef = "nearest_tss", qc_plots = FALSE, out_name = NULL, n_cores = 1)
results.pe = results$results
print(results.pe[1:5,1:5])

## ----warning = FALSE, message = FALSE-----------------------------------------
gs_path = system.file('extdata','vignette_genesets.txt', package='chipenrich')
results = polyenrich(peaks = peaks_E2F4, genome = 'hg19', genesets = gs_path, method="polyenrich_weighted", locusdef = "enhancer_plus5kb", qc_plots = FALSE, out_name = NULL, n_cores = 1)
results.pe = results$results
print(results.pe[1:5,1:5])

## ----warning = FALSE, message = FALSE-----------------------------------------
gs_path = system.file('extdata','vignette_genesets.txt', package='chipenrich')
results = hybridenrich(peaks = peaks_E2F4, genome = 'hg19', genesets = gs_path, locusdef = "nearest_tss", qc_plots = F, out_name = NULL, n_cores = 1)
results.hybrid = results$results
print(results.hybrid[1:5,1:5])

## ----warning = FALSE, message = FALSE-----------------------------------------
gs_path = system.file('extdata','vignette_genesets.txt', package='chipenrich')
results.prox = proxReg(peaks_E2F4, reglocation = 'tss',	genome = 'hg19', genesets=gs_path, out_name=NULL)
results.prox = results.prox$results
print(results.prox[1:5,1:7])

## ----fig.align='center', fig.cap='E2F4 peak distances to TSS', fig.height=6, fig.width=6, fig.show='hold', warning = FALSE, message = FALSE----
# Output in chipenrich and polyenrich
plot_dist_to_tss(peaks = peaks_E2F4, genome = 'hg19')

## ----fig.align='center', fig.cap='E2F4 chipenrich spline without mappability', fig.height=6, fig.width=6, fig.show='hold', warning = FALSE, message = FALSE----
# Output in chipenrich
plot_chipenrich_spline(peaks = peaks_E2F4, locusdef = 'nearest_tss', genome = 'hg19')

## ----fig.align='center', fig.cap='E2F4 polyenrich spline without mappability', fig.height=6, fig.width=6, fig.show='hold', warning = FALSE, message = FALSE----
# Output in polyenrich
plot_polyenrich_spline(peaks = peaks_E2F4, locusdef = 'nearest_tss', genome = 'hg19')

## ----fig.align='center', fig.cap='H3K4me3 gene coverage', fig.height=6, fig.width=6, fig.show='hold', warning = FALSE, message = FALSE----
# Output in broadenrich
plot_gene_coverage(peaks = peaks_H3K4me3_GM12878, locusdef = 'nearest_tss',  genome = 'hg19')

## -----------------------------------------------------------------------------
head(results$peaks)

## -----------------------------------------------------------------------------
head(results$peaks_per_gene)

## -----------------------------------------------------------------------------
head(results$results)

## ----warning = FALSE, message = FALSE-----------------------------------------
# Assessing if alpha = 0.05
gs_path = system.file('extdata','vignette_genesets.txt', package='chipenrich')
results = chipenrich(peaks = peaks_E2F4, genome = 'hg19', genesets = gs_path,
	locusdef = "nearest_tss", qc_plots = FALSE, randomization = 'complete',
    out_name = NULL, n_cores = 1)
alpha = sum(results$results$P.value < 0.05) / nrow(results$results)
# NOTE: This is for
print(alpha)

