assign_SN_SN {polymapR}

Assign (leftover) 1.0 markers

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)