overviewSNlinks: Plotting 1.0 links between homologues

In polymapR: Linkage Analysis in Outcrossing Polyploids

Plotting 1.0 links between homologues

Description

overviewSNlinks is written to enable merging of homologue fractions. Fractions of homologues will have more markers in coupling than in repulsion, whereas separate homologues will only have markers in repulsion.

Usage

overviewSNlinks(
  linkage_df,
  LG_hom_stack,
  LG,
  LOD_threshold,
  ymax = NULL,
  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 a column "SxN_Marker" specifying markernames, a column "homologue" specifying homologue cluster and "LG" specifying linkage group.
LG	Integer. Linkage group number of interest.
LOD_threshold	Numeric. LOD threshold of linkages which are plotted.
ymax	Maximum y-limit of the plots.
log	Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

Examples

data("SN_SN_P1", "LGHomDf_P1_1")
overviewSNlinks(linkage_df=SN_SN_P1,
               LG_hom_stack=LGHomDf_P1_1,
               LG=5,
               LOD_threshold=3)

polymapR documentation built on Nov. 5, 2023, 1:09 a.m.