finish_linkage_analysis: Linkage analysis between all markertypes within LG.
In mdavy86/polymapR: Linkage Analysis in Outcrossing Polyploids

Description Usage Arguments Value Examples

finish_linkage_analysis is a wrapper for linkage. Performs linkage calculations between all markertypes within a linkage group.

finish_linkage_analysis(marker_assignment, dosage_matrix,
  marker_combinations = NULL, target_parent = "P1", other_parent = "P2",
  convert_palindrome_markers = TRUE, ploidy = 4, ploidy2 = NULL,
  pairing = c("random", "preferential"), prefPars = c(0, 0), LG_number,
  verbose = TRUE, log = NULL, ...)

`marker_assignment`	A marker assignment matrix with markernames as rownames and at least containing the column `"Assigned_LG"`.
`dosage_matrix`	An integer matrix with markers in rows and individuals in columns.
`marker_combinations`	A matrix with four columns specifying marker combinations to calculate linkage. If NULL all combinations are used for which there are rf functions. Dosages of markers should be in the same order as specified in the names of rf functions. E.g. if using 1.0_2.0 and 1.0_3.0 types use: `matrix(c(1,0,2,0,1,0,3,0), byrow = TRUE, ncol = 4)`
`target_parent`	Character string specifying target parent.
`other_parent`	Character string specifying other parent.
`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?
`ploidy`	Ploidy level of parent 1.
`ploidy2`	Integer, by default `NULL`. If parental ploidies differ, the ploidy of parent 2.
`pairing`	Type of pairing at meiosis, with options `"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.
`LG_number`	Number of linkage groups (chromosomes).
`verbose`	Should messages be send to stdout or log?
`log`	Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.
`...`	(Other) arguments passed to `linkage`

Returns a matrix with marker assignments. Number of linkages of 1.0 markers are artificial.

## Not run: 
data("screened_data3", "marker_assignments_P1")
linkages_list_P1<-finish_linkage_analysis(marker_assignment=marker_assignments_P1,
                                              dosage_matrix=screened_data3,
                                              target_parent="P1",
                                              other_parent="P2",
                                              convert_palindrome_markers=FALSE,
                                              ploidy=4,
                                              pairing="random",
                                              LG_number=5)
                                              
## End(Not run)