finish_linkage_analysis is a wrapper for linkage, or in the case of probabilistic genotypes, linkage.gp.
The function performs linkage calculations between all markertypes within a linkage group.
finish_linkage_analysis(
input_type = "discrete",
marker_assignment,
dosage_matrix,
probgeno_df,
chk,
marker_combinations = NULL,
parent1 = "P1",
parent2 = "P2",
which_parent = 1,
ploidy,
ploidy2 = NULL,
convert_palindrome_markers = TRUE,
pairing = "random",
prefPars = c(0, 0),
LG_number,
verbose = TRUE,
log = NULL,
...
)Returns a matrix with marker assignments. Number of linkages of 1.0 markers are artificial.
Can be either one of 'discrete' or 'probabilistic'. For the former (default), dosage_matrix must be supplied,
while for the latter probgeno_df and chk must be supplied.
A marker assignment matrix with markernames as rownames and at least containing the column "Assigned_LG".
A named integer matrix with markers in rows and individuals in columns.
A data frame as read from the scores file produced by function
saveMarkerModels of R package fitPoly, or alternatively, a data frame containing the following columns:
Name of the sample (individual)
Name of the marker
Probabilities of dosage score '0'
Probabilities of dosage score '1' etc. (up to max dosage, e.g. P4 for tetraploid population)
Maximum genotype probability identified for a particular individual and marker combination
Most probable dosage for a particular individual and marker combination
Most probable dosage for a particular individual and marker combination, if maxP exceeds a user-defined threshold (e.g. 0.9), otherwise NA
Output list as returned by function checkF1. This argument is only needed if probabilistic genotypes are used.
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)
Character string specifying the identifier of parent 1, by default "P1"
Character string specifying the identifier of parent 2, by default "P2"
Integer, either 1 or 2, with default 1, where 1 or 2 refers to parent1 or parent2 respectively.
Integer ploidy level of parent1, and also by default parent2. Argument ploidy2 can be used if parental ploidies differ.
Integer, by default NULL. If parental ploidies differ, use this to specify the ploidy of parent2.
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?
Type of pairing at meiosis, with options "random" or "preferential". By default, random pairing is assumned.
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.
Number of linkage groups (chromosomes).
Should messages be sent to stdout or 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
if (FALSE) {
data("screened_data3", "marker_assignments_P1")
linkages_list_P1<-finish_linkage_analysis(marker_assignment=marker_assignments_P1,
dosage_matrix=screened_data3,
parent1="P1",
parent2="P2",
which_parent=1,
convert_palindrome_markers=FALSE,
ploidy=4,
pairing="random",
LG_number=5)
}
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