dataReading: Function to import sequencing results in R

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

Description

Sequencing results should be converted to datafiles with numbers of sequences mapped on each nucleotide in the reference genome. These files can be generated from indexed BAM files (mapping results) using the "genomeCoverageBed" tool available from the BEDTOOLS suite [1]. More information concerning file descriptions can be found online:

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

File format should be as follows (chromosome, position, number of sequences):

chrI	1	4
chrI	2	4
chrI	3	4
chrI	4	4
chrI	5	7
chrI	6	7
chrI	7	9
chrI	8	9
chrI	9	10
chrI	10	13

Usage

dataReading(IPfile, controlFile, yeastSpecies = NULL)

Arguments

IPfile	Name of the file with sequencing results related to IP sample
controlFile	Name of the file with sequencing results related to control sample
yeastSpecies	Not mandatory. Annotations to be used for locations of peaks in promoters. Annotations of CDS are available in bPeaks for yeasts: Debaryomyces.hansenii, Eremothecium.gossypii, Kluyveromyces.lactis, Pichia.sorbitophila, Saccharomyces.kluyveri, Yarrowia.lipolytica, Zygosaccharomyces.rouxii, Saccharomyces.cerevisiae, Candida.albicans, Candida.glabrata (see data yeastCDS)

Details

To obtain a required file from a BAM file (resultFile.bam), the command line is (SHELL):

genomeCoverageBed -ibam resultFile.bam -d > resultFile.txt

More information concerning file conversions can be found online:

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

Value

A list with three elements ($IPdata, $controlData, $cdsPositions): IP data, control data and (if specified by user) CDS positions for locations of peaks in promoters.

Note

Conversion of file formats regarding sequencing results can be a tricky task. Detailed information can be found online http://bpeaks.gene-networks.net/. Don't hesitate to contact us for further discussions.

Author(s)

Gaelle LELANDAIS

References

[1] Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841 842.

See Also

peakLocation dataPDR1 yeastCDS

Examples

# get library
library(bPeaks)

## Not run: 
# Sequencing result files associated to PDR1 datasets (IP and control files) 
# can be downloaded from our website http://bpeaks.gene-networks.net/. 
# They are respectively named "IP_genomeCoverage.txt" (IP sample) and 
# "INPUT_genomeCoverage.txt" (control sample).

# Import in R the sequencing results using S. cerevisiae CDS annotations.
data(yeastCDS)
seqResult = dataReading("IP_genomeCoverage.txt", "INPUT_genomeCoverage.txt",
			yeastSpecies = yeastCDS$Saccharomyces.cerevisiae)

# IP data
seqResult$IPdata

# control data
seqResult$controlData

# run peak detection from IP and control data (with default parameters)
bPeaksAnalysis(IPdata = seqResult$IPdata, 
	       controlData  = seqResult$controlData,
	       cdsPositions = seqResult$cdsPositions)

## End(Not run)

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