## ----getWin, message=FALSE,warning=FALSE--------------------------------------
library(strandCheckR)
files <- system.file(
    "extdata", c("s1.sorted.bam","s2.sorted.bam"), package = "strandCheckR"
    )
win <- getStrandFromBamFile(files, sequences = "10")
# shorten the file name
win$File <- basename(as.character(win$File))
win

## ----highestCoverage, eval=TRUE, message=FALSE,warning=FALSE------------------
head(win[order((win$NbPos+win$NbNeg),decreasing=TRUE),])

## ----paired end, eval=TRUE,message=FALSE,warning=FALSE------------------------
fileP <- system.file("extdata","paired.bam",package = "strandCheckR")
winP <- getStrandFromBamFile(fileP, sequences = "10")
winP$File <- basename(as.character(winP$File)) #shorten file name
winP

## ----intersect, eval=TRUE, warning=FALSE,message=FALSE------------------------
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
annot <- transcripts(TxDb.Hsapiens.UCSC.hg38.knownGene)
#add chr before the sequence names to be consistent with the annot data
win$Seq <- paste0("chr",win$Seq) 
win <- intersectWithFeature(
    windows = win, annotation = annot, overlapCol = "OverlapTranscript"
    )
win

## ----plotHist, eval=TRUE, message=FALSE,warning=FALSE-------------------------
plotHist(
    windows = win, groupBy = c("File","OverlapTranscript"), 
    normalizeBy = "File", scales = "free_y"
    )

## ----plotHistPaired, eval=TRUE,message=FALSE,warning=FALSE--------------------
plotHist(
    windows = winP, groupBy = "Type", normalizeBy = "Type", scales = "free_y"
    )

## ----heatMap, eval=TRUE, message = FALSE, warning=FALSE-----------------------
plotHist(
    windows = win, groupBy = c("File","OverlapTranscript"), 
    normalizeBy = "File", heatmap = TRUE
    )

## ----plotwin,eval=TRUE,message=FALSE,warning=FALSE----------------------------
plotWin(win, groupBy = "File")

## ----filterDNA, eval=TRUE, message=FALSE, warning=FALSE, results=FALSE--------
win2 <- filterDNA(
    file = files[2], sequences = "10", destination = "s2.filter.bam", 
    threshold = 0.7, getWin = TRUE
    )

## ----compare,eval=TRUE,message=FALSE,warning=FALSE----------------------------
win2$File <- basename(as.character(win2$File))
win2$File <- factor(win2$File,levels = c("s2.sorted.bam","s2.filter.bam"))
library(ggplot2)
plotHist(win2, groupBy = "File", normalizeBy = "File", scales = "free_y") +
    ggtitle("Histogram of positive proportions over all sliding windows before 
            and after filtering reads coming from double strand DNA")

## ----remove-bams, echo = FALSE------------------------------------------------
if (file.exists("s2.filter.bam")) unlink("s2.filter.bam")
if (file.exists("s2.filter.bam.bai")) unlink("s2.filter.bam.bai")

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

