peakLocation: Function to locate detected basic peaks (bPeaks) according to...

In bPeaks: bPeaks: an intuitive peak-calling strategy to detect transcription factor binding sites from ChIP-seq data in small eukaryotic genomes

Description

Starting from a BED file with positions of detected peaks and a table with positions of CDS (genes), this function allows to dentify the peaks that are located "upstream" or "in" annotated CDS. Annotations of CDS for different yeast species are available in bPeaks package (see data yeastCDS).

Usage

peakLocation(bedFile, cdsPositions, withoutOverlap = FALSE,
            outputName = "bPeaksLocation", promSize = 800)

Arguments

bedFile	Name of a BED file with positions of detected peaks (using bPeaks or another program)
cdsPositions	A table (matrix) with positions of CDS (genes). Four columns are required (chromosome, starting position, ending position, strand (W or C), description)
withoutOverlap	If TRUE, this option allows to filter peak that are located in a promoter AND a CDS.
outputName	Name for output files
promSize	Genomic size to be considered as promoter (upstream to CDS)

Details

More information can be found online http://bpeaks.gene-networks.net/.

Value

Graphics and text files (saved in the R working directory).

Note

Detailed information and tutorials can be found online http://bpeaks.gene-networks.net/.

Author(s)

Gaelle LELANDAIS

References

http://bpeaks.gene-networks.net/

See Also

bPeaksAnalysis dataReading yeastCDS

Examples

## Not run: 
# -> bPeaks analysis with (all chromosome and default parameters optimized for yeasts)

# STEP 1: get PDR1 data and annotations in yeasts
data(dataPDR1)
data(yeastCDS)

# STEP 2: bPeaks analysis
bPeaksAnalysis(IPdata = dataPDR1$IPdata, 
               controlData = dataPDR1$controlData, 
               windowSize = 150, windowOverlap = 50, 
               IPcoeff = 6, controlCoeff = 4, 
               log2FC = 2, averageQuantiles = 0.9,
               resultName = "bPeaks_PDR1", 
               peakDrawing = TRUE)

# STEP 3 : procedure to locate peaks according to 
# predefined chromosomal features
peakLocation(bedFile = "bPeaks_PDR1_bPeaks_allGenome.bed", 
            cdsPositions = yeastCDS$Saccharomyces.cerevisiae,
	    withoutOverlap = FALSE,
            outputName = "bPeakLocation_finalPDR1", promSize = 800)

## End(Not run)

bPeaks documentation built on May 1, 2019, 10:14 p.m.