overviewSNlinks {polymapR}

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)