mappoly (version 0.2.1)

import_phased_maplist_from_polymapR: Import phased map list from polymapR

Description

Function to import phased map lists from polymapR

Usage

import_phased_maplist_from_polymapR(maplist, mappoly.data, ploidy = NULL)

Arguments

maplist

a list of phased maps obtained using function create_phased_maplist from package polymapR

mappoly.data

a dataset used to obtain maplist, converted into class mappoly.data

ploidy

the ploidy level

References

Bourke PM et al: (2019) PolymapR <U+2014> linkage analysis and genetic map construction from F1 populations of outcrossing polyploids. _Bioinformatics_ 34:3496<U+2013>3502. https://doi.org/10.1093/bioinformatics/bty1002

Mollinari, M., and Garcia, A. A. F. (2019) Linkage analysis and haplotype phasing in experimental autopolyploid populations with high ploidy level using hidden Markov models, _G3: Genes, Genomes, Genetics_. https://doi.org/10.1534/g3.119.400378

Examples

# NOT RUN {
require(polymapR)
## Loading polymapR example
data("integrated.maplist", "screened_data3", "marker_assignments_P1","marker_assignments_P2")
maplist <- 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)
 ## Importing polymapR dataset                                
 mappoly.data <- import_data_from_polymapR(screened_data3, 4)
 plot(mappoly.data) 
 
 ## Importing polymapR phased maplist
 mappoly.maplist <- import_phased_maplist_from_polymapR(maplist, mappoly.data)
 plot_map_list(mappoly.maplist)
 ## plot phased map
 plot(mappoly.maplist[[1]])
 ## plot a segment of phased map (from 0 to 20 cM)
 plot(mappoly.maplist[[1]], mrk.names = TRUE, left.lim = 0, right.lim = 20, cex = .7)

# }