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DQRECOMBINATIONS procedure

Plots a matrix of recombination frequencies between markers (S.J. Welham & D.A. Murray).

Options

DCHROMOSOMES = scalar, variate or text Specifies a subset of the linkage groups to be displayed
TITLE = text General title for the plot
WINDOW = scalar Window number for the graph; default 1
KEYWINDOW = scalar Window number for the key (zero for no key); default 2
PALETTE = string token Colour scheme for plot (colour, color, greyscale, grayscale); default colo

Parameters

RECFREQUENCIES = symmetric matrices Recombination frequencies to plot
CHROMOSOMES = factors Linkage group for each marker

Description

DQRECOMBINATIONS plots the recombination frequencies between markers in a shade diagram. The RECFREQUENCIES parameter must specify the recombination frequencies, in a symmetric matrix with each row representing a marker. The linkage groups for each marker can be supplied, in a factor, using the CHROMOSOMES parameter.

The DCHROMOSOMES option allows you to display a subset of the linkage groups. The setting can be either a variate or a scalar referring to the levels of the CHROMOSOMES factor, or a text referring to its labels.

The TITLE, WINDOW, and KEYWINDOW options can specify a title, the plotting window, and the key window. The PALETTE option controls the colour scheme used in the shade diagram.

Options: DCHROMOSOMES, TITLE, WINDOW, KEYWINDOW, PALETTE.

Parameters: RECFREQUENCIES, CHROMOSOMES.

Action with RESTRICT

Restrictions are not allowed.

See also

Procedure: QRECOMBINATIONS.

Commands for: Statistical genetics and QTL estimation, Graphics.

Example

CAPTION          'DQRECOMBINATIONS example'; STYLE=meta
QIMPORT          [POPULATION=F2] '%GENDIR%/Examples/F2maize_geno.txt';\
                 MKSCORES=mkscores; MKNAMES=mknames; PARENTS=parents
CALCULATE        nmarkers =  NVAL(mkscores)
CALCULATE        ngenotypes =  NVAL(mkscores[1])
QRECOMBINATIONS  [POPULATION=F2; PLOT=*; USEPENALTY=yes] mkscores;\
                 NRECOMBINATIONS=TwopNrec; RECFREQUENCIES=TwopRecfreq;\
                 MKNAMES=mknames; PARENTS=parents
DQRECOMBINATIONS TwopRecfreq
Updated on June 20, 2019

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