createMap: Marker ordering function

In mdavy86/polymapR: Linkage Analysis in Outcrossing Polyploids

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)
                             
## End(Not run)

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