polymapR (version 1.0.17)

orient_and_merge_maps: Align and integrate maps

Description

Align homologues to the same orientation and integrates maps using LPmerge

Usage

orient_and_merge_maps(maplist_P1, maplist_P2, parent_ID_1 = "P1",
  parent_ID_2 = "P2", connection_threshold = 2, LPmerge_interval = 4,
  single_LPmerge = FALSE, plot_graph = FALSE, ploidy = 4, log = NULL)

Arguments

maplist_P1, maplist_P2

A list of length=ploidy, with data.frames containing markernames and position.

parent_ID_1, parent_ID_2

Character string with parent IDs

connection_threshold

The number of markers two homologues should have in common to have a significant connection

LPmerge_interval

The max.interval value used for LPmerge

single_LPmerge

Logical, by default FALSE. If TRUE then only a single merge with max.interval = LPmerge_interval will be run, otherwise all intervals up to LPmerge_interval will also be tested.

plot_graph

Should the connection network be drawn?

ploidy

The ploidy of the organism

log

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

Examples

# NOT RUN {
data("maplist_P1_subset")
data("maplist_P2_subset")
# }
# NOT RUN {
## Example temporarily suspended (April 2018): LPmerge CRAN issues
integrated_map_LG2<-orient_and_merge_maps(maplist_P1=maplist_P1_subset[["LG4"]],
                                            maplist_P2=maplist_P2_subset[["LG4"]],
                                            plot_graph = TRUE)
# }