Linkage {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')