Testing sample independence from genotype counts
chiCalc carries out Fisher's exact tests of sample independence using genotype data.
chiCalc(infile = NULL, outfile = NULL, pairwise = FALSE, mcRep = 2000)
infile |
A character string indicating the location and name of a genepop format file to be read. If the file is in the current working directory, only the name must be provided. If the file is in a directory other than the current working directory, either a relative or absolute path to the file must be provided. The genepop file can be in the 2-digit or 3-digit allele format. |
outfile |
A character string indicating the prefix to be added to the results directory created. All results files will be written to this directory. |
pairwise |
A logical argument indicating whether sample independence should be tested between all population pairs. |
mcRep |
An integer specifying the number Monte Carlo test replicates. See |
All results will be written to a user defined folder ("working_directory/outfile"), providing an argument is passed for 'outfile'. Otherwise, results will only be returned to the workspace.
Fisher's exact tests are carried out using the function fisher.test. Multilocus p values are calculated using Fisher's method for combining p value.
overall |
A data frame containing p values calculated across all population samples, per locus and across all loci. |
multilocus_pw |
Generated if |
locus_pw |
A dataframe containing locus p values calculated for all pairs of populations. Rows represent loci, while columns represent pairwise comparisons. |
Kevin Keenan <kkeenan02@qub.ac.uk>
## Not run:
# To run an example use the following format
library(diveRsity)
data(Test_data)
test_results <- chiCalc(infile = Test_data, outfile = NULL,
pairwise = TRUE, mcRep = 5000)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.