orient_and_merge_maps: Align and integrate maps

In mdavy86/polymapR: Linkage Analysis in Outcrossing Polyploids

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

data("maplist_P1_subset")
data("maplist_P2_subset")
integrated_map_LG2 <- orient_and_merge_maps(maplist_P1=maplist_P1_subset[["LG4"]],
                                            maplist_P2=maplist_P2_subset[["LG4"]],
                                            plot_graph = TRUE)

mdavy86/polymapR documentation built on May 25, 2019, 9:35 p.m.