Statistical methods for building random transposon mutagenesis libraries.
ABSTRACT During the construction of random transposon mutagenesis libraries, four essential statistical issues arise: (1) Computing basic probability results for number of open reading frame knockouts. (2) Estimating the number of new open reading frames that will be knockouts in the next set of clones. (3) Estimating the number of essential open reading frames. (4) Computing the probability that an open reading frame is essential given the distribution of insertions. This chapter examines these issues and evaluates potential solutions using three different approaches: Efron and Thisted's estimator, Will and Jacobs's parametric bootstrap, and Blades and Broman's Gibbs sampler. In doing so, this chapter provides guidance for using the R statistical project to solve these problems.