[BioC] BAM files to Genomic Ranges object

[Dario Strbenac]

>cpdens <- cpgDensityCalc(gr_list, organism=Mmusculus, window =600)

This example doesn't make biological sense to me. This creates a 600 base window around the start of each sequencing read. The window argument is relevant if you have a data.frame of genes, and you'd like to know the CpG density in a window around the TSS, for example.

For your purpose, I would recommend

cpdens <- cpgDensityCalc(gr_list, organism=Mmusculus, seq.len = aveLength)

The average DNA fragment length that was sequenced is assigned to aveLength. Ask the biologist who prepared the sequencing library for this information. It is related to the position on the gel that they cut the DNA out.

See http://nar.oxfordjournals.org/content/40/10/e72.full for more background.

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Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia