create_phased_maplist {polymapR} | R Documentation |
Create a phased homologue map list using the original dosages
Description
create_phased_maplist
is a function for creating a phased maplist, using
integrated map positions and original marker dosages.
Usage
create_phased_maplist(
input_type = "discrete",
maplist,
dosage_matrix.conv,
dosage_matrix.orig = NULL,
probgeno_df,
chk,
remove_markers = NULL,
original_coding = FALSE,
N_linkages = 2,
lower_bound = 0.05,
ploidy,
ploidy2 = NULL,
marker_assignment.1,
marker_assignment.2,
parent1 = "P1",
parent2 = "P2",
marker_conversion_info = NULL,
log = NULL,
verbose = TRUE
)
Arguments
input_type |
Can be either one of 'discrete' or 'probabilistic'. For the former (default), at least |
maplist |
A list of maps. In the first column marker names and in the second their position. |
dosage_matrix.conv |
Matrix of marker dosage scores with markers in rows and individuals in columns. Note that dosages must be
in converted form, i.e. after having run the |
dosage_matrix.orig |
Optional, by default |
probgeno_df |
Probabilistic genotypes, for description see e.g. |
chk |
Output list as returned by function |
remove_markers |
Optional vector of marker names to remove from the maps. Default is |
original_coding |
Logical. Should the phased map use the original marker coding or not? By default |
N_linkages |
Number of significant linkages (as defined in |
lower_bound |
Numeric. Lower bound for the rate at which homologue linkages (fraction of total for that marker) are recognised. |
ploidy |
Integer. Ploidy of the organism. |
ploidy2 |
Optional integer, by default |
marker_assignment.1 |
A marker assignment matrix for parent 1 with markernames as rownames and at least containing the column |
marker_assignment.2 |
A marker assignment matrix for parent 2 with markernames as rownames and at least containing the column |
parent1 |
character vector with names of the samples of parent 1 |
parent2 |
character vector with names of the samples of parent 2 |
marker_conversion_info |
One of the list elements (named 'marker_conversion_info') generated by the function |
log |
Character string specifying the log filename to which standard output should be written. If |
verbose |
Logical, by default |
Examples
## Not run:
data("integrated.maplist", "screened_data3", "marker_assignments_P1","marker_assignments_P2")
create_phased_maplist(maplist = integrated.maplist,
dosage_matrix.conv = screened_data3,
marker_assignment.1=marker_assignments_P1,
marker_assignment.2=marker_assignments_P2,
ploidy = 4)
## End(Not run)