bootstrapHet: Calculate confidence intervals on observed and expected...

In PopGenKit: Useful functions for (batch) file conversion and data resampling in microsatellite datasets

Description

This function uses a Arlequin project file (.arp) as input. For each population, it resamples individuals with replacement (i.e. bootstrap resampling) and calculates the corresponding confidence intervals on Ho (observed heterozygosity) and He (expected heterozygosity).

Usage

bootstrapHet(datafile, ndigit = 3, nrepet = 1000)

Arguments

datafile	Name of the Arlequin file to use as input, with the extension (e.g. 'glyptemys3.arp')
ndigit	Number of digits per allele in input file. Can be 2 or 3 (default is 3)
nrepet	Number of bootstrap replicates to perform. Default is 1000. Can be slow for large datafiles.

Details

Some .arp files might not be imported correctly depending on which software was used to generate them. If this is the case, start from the Genepop file and convert it first with convert.

It is possible to perform bootstrapping on markers instead of individuals. To do so, use the function bootstrapHet_byloc instead.

Value

Results are printed to a file saved in the working directory, with the suffix 'bootHet' in the filename. First part of the table reports real Ho and He values for each locus in each population. Bottom part reports bootstrap results for each population: mean calculated Ho and He as well as the lower and upper bounds of their 95 % confidence intervals.

Author(s)

Sebastien Rioux Paquette

References

Excoffier, L. and H.E.L. Lischer (2010). Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Res. 10: 564-567.

Rousset, F. (2008). Genepop'007: a complete reimplementation of the Genepop software for Windows and Linux. Mol. Ecol. Res. 8: 103-106.

See Also

bootstrapHet_byloc, convert

PopGenKit documentation built on May 2, 2019, 3:33 p.m.