# Calculate strandness information of a bam file

## Documentation for package ‘strandCheckR’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

strandCheckR-package | Quantify and Filter putative double strand DNA from strand-specific RNA bam file
calculateStrandCoverage | Calculate the strand information based on coverage
calculateStrandNbReads | Calculate the strand information based the number of reads
checkPairedEnd | Test whether a bam file if single end or paired end
concatenateAlignments | Concatenate a list of Alignments into One
filterDNA | Filter Double Strand Sequences from a Bam File
getWinFromBamFile | get the strand information of all windows from bam files
getWinFromGranges | Get the Sliding Windows from a GRanges object
getWinFromIRanges | Get the Ranges of Sliding Windows from an IRanges object
getWinFromReadInfo | get the strand information of all windows from read information
getWinOfAlignments | get the window ranges of alignments
intersectWithFeature | Intersect the windows data frame with an annotation data frame
keptProbaWin | get the probability of begin kept for each window
keptReadFragment | calculate the read fragments to be kept
plotHist | Plot the histogram of positive proportions
plotWin | Plot the Proportion of + Stranded Reads
strandCheckR | Quantify and Filter putative double strand DNA from strand-specific RNA bam file
summarizeHist | Summarize the histogram of strand proportions from the input windows data frame