assign_SN_SN: Assign (leftover) 1.0 markers

In mdavy86/polymapR: Linkage Analysis in Outcrossing Polyploids

Description

Some 1.0 markers might have had ambiguous linkages, or linkages with low LOD scores leaving them unlinked to a linkage group. assign_SN_SN finds 1.0 markers unlinked to a linkage group and tries to assign them.

Usage

assign_SN_SN(linkage_df, LG_hom_stack, LOD_threshold, ploidy, LG_number,
  log = NULL)

Arguments

linkage_df	A data.frame as output of linkage with arguments markertype1=c(1,0) and markertype2=NULL.
LG_hom_stack	A data.frame with markernames ("SxN_Marker"), linkage group ("LG") and homologue ("homologue")
LOD_threshold	A LOD score at which linkages between markers are significant.
ploidy	Integer. The ploidy level of the plant species.
LG_number	Integer. Number of chromosomes (linkage groups)
log	Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

Value

Returns a data.frame with the following columns:

SxN_Marker	The markername
Assigned_hom1	The assigned homologue
Assigned_LG	The assigned linkage group

Examples

data("SN_SN_P1", "LGHomDf_P1_1")
SN_assigned<-assign_SN_SN(linkage_df = SN_SN_P1,
             LG_hom_stack = LGHomDf_P1_1,
             LOD_threshold= 4,
             ploidy=4,
             LG_number=5)

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