bPeaks (version 1.0)

peakLocation: Function to locate detected basic peaks (bPeaks) according to predifined chromosomal features

Description

Starting from a BED file with positions of detected peaks and a file with positions of particular chromosomal features (genes for instance), this function allows to dentify the peaks that are located "before", "after" or "in" the chromosomal features.

Usage

peakLocation(bedFile, chromosomalFeatureFile = "", genomicInfo = NULL, 
            outputName = "bPeakLocation", promSize = 800)

Arguments

bedFile

Name of a BED file with positions of detected peaks (using bPeaks or another program)

chromosomalFeatureFile

Name of a file with positions of particular chromosomal features. This file must comprise four columns (chromosome, starting position, ending position, description)

genomicInfo

A table with four columns (chromosome, starting position, ending position, description). This table should have been created with the dataReading function

outputName

Name for output files

promSize

Genomic size to be considered "before" and "after" the chromosomal features

Value

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

Details

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

References

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

See Also

bPeaksAnalysis dataReading

Examples

# -> bPeaks analysis with (all chromosome and default parameters optimized for yeasts)

# STEP 1: get PDR1 data (ChIP-seq experiments - IP and control samples - 
# with transcription factor Pdr1 in yeast Saccharomyces cerevisiae) 
data(dataPDR1)

# 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", 
            genomicInfo = dataPDR1$chromosomalFeatures,
            outputName = "bPeakLocation_finalPDR1", promSize = 800)