bPeaks (version 1.2)

peakDrawing: Function to draw graphical representations of genomic regions detected using bPeaks methodology

Description

This function allows to create PDF files, with graphical representations of the detected basic peaks (bPeaks). Genomic regions are shown together with the values of the parameters used to detect the region.

Usage

peakDrawing(vecIP, vecControl, lineIP, lineControl, lineFC, lineAverage,  posInf = 1, posSup = NULL, add = 10, title = "")

Arguments

vecIP

Vector with sequencing depth at each nucleotide (from start pos = 1 to end)

vecControl

Vector with sequencing depth at each nucleotide (from start pos = 1 to end)

lineIP

Threshold values used for peak detection (IP signal)

lineControl

Threshold values used for peak detection (control signal)

lineFC

Threshold values used for peak detection (log2(IP/control) values)

lineAverage

Threshold values used for peak detection (average log2(IP) and log2(control) values)

posInf

Genomic position to start the representation

posSup

Genomic position to end the representation

add

Number of bases before and after posInf and posSup to add

title

Graphic main title

Value

Image in x11() terminal

Details

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

References

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

See Also

bPeaksAnalysis

Examples

# get library 
library(bPeaks)

# get PDR1 data
data(dataPDR1)

# IP signal (smoothed) - Chromosome IV
IPsignal = dataSmoothing(dataPDR1$IPdata[dataPDR1$IPdata[,1] == "chrIV",3], 20)
# control signal (smoothed)
controlSignal = dataSmoothing(dataPDR1$controlData[dataPDR1$controlData[,1] == "chrIV",3], 20)

# draw all chromosome
peakDrawing(vecIP = IPsignal, vecControl = controlSignal, 
            lineIP = 0, lineControl = 0, lineFC = 0, lineAverage = 0, 
            posInf = 465000, posSup = 465550, 
            add = 10, title = "PDR1 data - chromosome #4")