bPeaks (version 1.2)

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

Description

bPeaks is a simple approach to identify transcription factor binding sites from ChIP-seq data. Our general philosophy is to provide an easy-to-use tool, well-adapted for small eukaryotic genomes (< 20 Mb). bPeaks uses a combination of 4 cutoffs (T1, T2, T3 and T4) to mimic "good peak" properties as described by biologists who visually inspect the ChIP-seq data on a genome browser. For yeast genomes, bPeaks calculates the proportion of peaks that fall in promoter sequences. These peaks are good candidates as transcription factor binding sites.

Details

Package:

bPeaks

Type:

Package

Version:

1.2

Date:

2014-02-28

License:

GPL

References

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

See Also

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

Examples

# get library
library(bPeaks)

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

# STEP 2 : bPeaks analysis (only 10 kb of chrIV are analyzed here, 
#          as an illustration)
bPeaksAnalysis(IPdata = dataPDR1$IPdata[40000:50000,], 
               controlData  = dataPDR1$controlData[40000:50000,], 
	       cdsPositions = dataPDR1$cdsPositions,
               windowSize = 150, windowOverlap = 50, 
               IPcoeff = 4, controlCoeff = 2, 
	       log2FC  = 1, averageQuantiles = 0.5,
               resultName = "bPeaks_example")

# --> Result files (PDF and BED) are written in the working directory.

## Not run: 
# # -> bPeaks analysis, all chromosome IV and default parameters (optimized for yeasts)
# 
# # STEP 1: get PDR1 data (ChIP-seq experiments, IP and control samples, 
# # 	related to the transcription factor Pdr1 in yeast Saccharomyces 
# # 	cerevisiae) 
# data(dataPDR1)
# 
# # STEP 2: bPeaks analysis
# bPeaksAnalysis(IPdata = dataPDR1$IPdata, 
#                controlData  = dataPDR1$controlData,
# 	       cdsPositions = dataPDR1$cdsPositions, 
#                windowSize = 150, windowOverlap = 50, 
#                IPcoeff = 2, controlCoeff = 2, 
#                log2FC = 2, averageQuantiles = 0.9,
#                resultName = "bPeaks_PDR1", 
#                peakDrawing = TRUE)
# 
# # STEP 3 : procedure to locate peaks according to 
# # 	   gene positions
# peakLocation(bedFile = "bPeaks_PDR1_bPeaks_allGenome.bed", 
#             cdsPositions = yeastCDS$Saccharomyces.cerevisiae,
#             outputName = "bPeakLocation_finalPDR1", promSize = 800)
# 
# # -> Note that cds (genes) positions are stored in bPeaks package for several yeast
# # species
# data(yeastCDS)
# 
# summary(yeastCDS)
# #                         Length Class      Mode     
# # Debaryomyces.hansenii    31370  -none-     character
# # Eremothecium.gossypii    23615  -none-     character
# # Kluyveromyces.lactis     25380  -none-     character
# # Pichia.sorbitophila      55875  -none-     character
# # Saccharomyces.kluyveri   27790  -none-     character
# # Yarrowia.lipolytica      32235  -none-     character
# # Zygosaccharomyces.rouxii 24955  -none-     character
# # Saccharomyces.cerevisiae     5  data.frame list     
# # Candida.albicans             5  data.frame list     
# # Candida.glabrata             5  data.frame list
# ## End(Not run)