peakDrawing: Function to draw graphical representations of genomic regions...

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

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

Details

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

Value

Image in x11() terminal

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

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")

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