baseLineCalc: Function to calculate the average number of reads mapped on...
In bPeaks: bPeaks: an intuitive peak-calling strategy to detect transcription factor binding sites from ChIP-seq data in small eukaryotic genomes

Description Usage Arguments Details Value Note Author(s) References See Also Examples

This function calculates the mean genome-wide read depth.

1	baseLineCalc(covData)

covData

A vector with the numbers of sequences aligned at each genomic position to be considered in the analysis

This function adds the numbers of sequences observed at each position and divides this number by the genome size (total number of nucleotides).

The average number of reads mapped on each nucleotide in the genome.

Detailed information and tutorials can be found online http://bpeaks.gene-networks.net/.

Gaelle LELANDAIS

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

bPeaksAnalysis

# get library
library(bPeaks)

# get PDR1 data
data(dataPDR1)

# mean genome-wide read depth in IP data
meanIPcov = baseLineCalc(dataPDR1$IPdata[,3])
print(meanIPcov)

# mean genome-wide read depth in control data
meanContCov = baseLineCalc(dataPDR1$controlData[,3])
print(meanContCov)