statsContig: Compute summary statistics from observed data

In poolABC: Approximate Bayesian Computation with Pooled Sequencing Data

Compute summary statistics from observed data

Description

Computes a defined set of summary statistics from observed data. Those summary statistics can then be used as the target for parameter estimation or model selection with Approximate Bayesian Computation.

Usage

statsContig(randomWindows, nPops, stat.names = NA)

Arguments

randomWindows	a list with randomly selected loci of observed data. This list should contain five elements: freqs, positions, rMajor, rMinor and coverage. Each of those elements should contain one entry per locus with the appropriate information.
nPops	is an integer indicating how many different populations are present in the dataset you are analysing.
stat.names	optional character vector with the names of the summary statistics from the simulated data. If available, these names will be added to the summary statistics computed from the observed data.

Details

Summary statistics are computed for a given subset of the data. Ideally, this subset is composed of randomly selected windows of the observed data. Those random windows should be selected from multiple contigs, treating each contig as a different locus.

Value

a vector of observed summary statistics. These summary statistics are computed from blocks of observed data present in the randomWindows input argument. If the stat.names input argument is available, the summary statistics will be named.

poolABC documentation built on Aug. 8, 2023, 5:14 p.m.