polymapR (version 1.0.17)

createMap: Marker ordering function

Description

Creates a linkage map from a .pwd file using the weighted regression algorithm employed by JoinMap

Usage

createMap(pwdDATA, parent_ID = "P1", chm_num, h_num, mapFun = c("haldane",
  "kosambi"), jumpThresh = 5, max_rf = 0.4, min_LOD = 1, rippleFREQ = 1,
  rippleRounds = 3, round3 = TRUE, printMAPS = FALSE, log = NULL)

Arguments

pwdDATA

pwd data.frame giving pairwise r and LOD estimates.

parent_ID

Identifier of the parent for which the map belongs

chm_num

The number of the chromosome being mapped

h_num

The number of the homologue being mapped

mapFun

The mapping function to use. Currently Haldane and Kosambi are available.

jumpThresh

The "Jump" threshold to use (normalised comparison of G2 values), with default value 5 as employed by JoinMap.

max_rf

The maximum recombination frequency to use in the mapping, default 0.4

min_LOD

The minimum LOD to use in the mapping, default is 1

rippleFREQ

How often to ripple (every added marker? every 2 markers?)

rippleRounds

The number of rounds of rippling to be attempted

round3

Option to stop mapping after two rounds. Default is TRUE, so 3 rounds.

printMAPS

Allows the user to see maps developing, default is FALSE.

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("all_linkages_list_P1_subset")
map_P1_LG2_hom3 <- createMap(pwdDATA=all_linkages_list_P1_subset[["LG2"]][["homologue3"]],
                             parent_ID = "P1",
                             chm_num=2,
                             h_num=3,
                             mapFun = "haldane",
                             jumpThresh = 5,
                             max_rf = 0.4,
                             min_LOD = 1,
                             rippleFREQ = 1,
                             rippleRounds = 3,
                             round3 = TRUE,
                             printMAPS = FALSE,
                             log = NULL)
                             
# }