defaultErrorProb: Replacement probabilities for sequencing errors
In ChIPsim: Simulation of ChIP-seq experiments

Description Usage Details Value Author(s) References Examples

For each nucleotide this function provides probabilities indicating how likely it is to be replaced by any of the other nucleotides should a sequencing error occur.

1	defaultErrorProb()

The probabilities used here are the ones determined by Dohm et al. for Beta vulgaris. They should be more appropriate than a uniform distribution but the use of species specific rates is recommended where available.

A list of four vectors with replacement probabilities for each nucleotide.

Peter Humburg

Juliane C. Dohm, Claudio Lottaz, Tatiana Borodina, and Heinz Himmelbauer. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucl. Acids Res., pages gkn425+, July 2008.