Linkage: Tables and exact test for genotypic linkage disequilibrium

In genepop: Population Genetic Data Analysis Using Genepop

Tables and exact test for genotypic linkage disequilibrium

Description

Exact test for each pair of loci in each population. See this section of the Genepop executable documentation for more information on the statistical methods.

Usage

test_LD(
  inputFile,
  outputFile = "",
  settingsFile = "",
  dememorization = 10000,
  batches = 100,
  iterations = 5000,
  verbose = interactive()
)

write_LD_tables(inputFile, outputFile = "", verbose = interactive())

Arguments

inputFile	The path of the input file, in Genepop format
outputFile	character: The path of the output file
settingsFile	character: The path of the settings file
dememorization	integer: length of dememorization step of Markov chain algorithm
batches	integer: Number of batches
iterations	integer: Iterations per batch
verbose	logical: whether to print some information

Value

The path of the output file is returned invisibly.

Examples

## Not run:  # 'dontrun' only because a bit too slow for CRAN checks
locinfile <- genepopExample('sample.txt')
test_LD(locinfile,'sample.txt.DIS')
if ( ! interactive()) clean_workdir(otherfiles='sample.txt')

## End(Not run)
locinfile <- genepopExample('sample.txt')
write_LD_tables(locinfile,'sample.txt.TAB')
if ( ! interactive()) clean_workdir(otherfiles='sample.txt')

genepop documentation built on Jan. 22, 2023, 1:07 a.m.