seedy (version 1.3)

deepseqmat: Generate deep sequence observations

Description

Generates a matrix of polymorphism frequencies

Usage

deepseqmat(X)

Arguments

X

Simulated complete genomic sampling data from the simulateoutbreak or simulatepopulation functions.

Value

• Returns a matrix, each row represents a polymorphic site, each column a sample. Frequencies of the mutant type (relative to the initial strain) are reported.

Details

The argument full=TRUE must be passed to simulateoutbreak or simulatepopulation in order for complete genomic data to be generated for each sample. Data of this format can be passed to this function.

Examples

data(deepseq)
W <- deepseqmat(deepseq)