bPeaks (version 1.2)

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 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)

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 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)