linkage: Calculate recombination frequency, LOD and phase
In mdavy86/polymapR: Linkage Analysis in Outcrossing Polyploids

Description Usage Arguments Value Examples

linkage is used to calculate recombination frequency, LOD and phase within one type of marker or between two types of markers.

linkage(dosage_matrix, markertype1 = c(1, 0), markertype2 = NULL,
  target_parent = "P1", other_parent = "P2", G2_test = FALSE,
  convert_palindrome_markers = TRUE, LOD_threshold = 0, ploidy = c(4, 6),
  ploidy2 = NULL, pairing = c("random", "preferential"), prefPars = c(0,
  0), combinations_per_iter = NULL, verbose = TRUE, full_output = FALSE,
  iter_RAM = 500, ncores = 1, log = NULL)

`dosage_matrix`	An integer matrix with markers in rows and individuals in columns.
`markertype1`	A vector of length 2 specifying the first markertype to compare. The first element specifies the dosage in `target_parent`, the second in `other_parent`.
`markertype2`	A vector of length 2 specifying the first markertype to compare. This argument is optional. If not specified, the funciton will calculate linkage within the markertype as specified by `markertype1`. The first element specifies the dosage in `target_parent`, the second in `other_parent`.
`target_parent`	Character string specifying the target parent as provided in the columnnames of dosage_matrix
`other_parent`	Character string specifying the other parent as provided in the columnnames of dosage_matrix
`G2_test`	Apply a G2 test (LOD of indepedence) in addition to the LOD of linkage.
`convert_palindrome_markers`	Logical. Should markers that behave the same for both parents be converted to a workable format for that parent? E.g.: should 3.1 markers be converted to 1.3? If unsure, set to TRUE.
`LOD_threshold`	Minimum LOD score of linkages to report. Recommended to use for large number (> millions) of marker comparisons in order to reduce memory usage.
`ploidy`	Integer. The ploidy of parent 1.
`ploidy2`	Integer, by default `NULL`. If parental ploidies differ, the ploidy of parent 2.
`pairing`	Type of pairing. `"random"` or `"preferential"`.
`prefPars`	The estimates for preferential pairing parameters for parent 1 and 2, in range 0 <= p < 2/3. By default this is c(0,0) (so, no preferential pairing). See the function `test_prefpairing` and the vignette for more details.
`combinations_per_iter`	Optional integer. Number of marker combinations per iteration.
`verbose`	Should messages be send to stdout?
`full_output`	Logical, by default `FALSE`. If `TRUE`, the complete output over all phases and showing marker combination counts is returned.
`iter_RAM`	A (very) conservative estimate of working memory in megabytes used per core. It only takes the size frequency matrices into account. Actual usage is more, espacially with large number of linkages that are reported. Reduce memory usage by using a higher LOD_threshold.
`ncores`	Number of cores to use. Works both for Windows and UNIX (using `doParallel`). Use `parallel::detectCores()` to find out how many cores you have available.
`log`	Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

Returns a data.frame with columns:

`marker_a`	first marker of comparison. If markertype2 is specified, it has the type of markertype1.
`marker_b`	second marker of comparison. It has the type of markertype2 if specified.
`r`	(estimated) recombinations frequency
`LOD`	(estimated) LOD score
`phase`	phase between markers

data("screened_data3")
SN_SN_P1 <- linkage(dosage_matrix = screened_data3,
                   markertype1 = c(1,0),
                   target_parent = "P1",
                   other_parent = "P2",
                   ploidy = 4,
                   pairing = "random",
                   ncores = 1
                   )