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DQMKSCORES procedure

Plots a grid of marker scores for genotypes and indicates missing data (D.A. Murray).


PLOT = string token Type of plot (missing, all); default miss
LOWERGENOTYPE = scalar Lower genotype for the display
UPPERGENOTYPE = scalar Upper genotype for the display
DCHROMOSOMES = variate, text or scalar Specify a subset of the linkage groups to be displayed
POPULATIONTYPE = string token Type of population (BC1, DH1, F2, RIL, BCxSy, AMP); must be set
COLOURS = text or variate Colours to use for the different marker scores
TITLE = text Title for the graph


MKSCORES= pointers Marker score code for each marker
CHROMOSOMES = factors Linkage group for each marker
PARENTS = pointers Parent information
IDPARENTS = texts Labels to identify the parents


DQMKSCORES produces graphical displays of marker scores for a set of genotypes. The marker scores should be supplied by setting the MKSCORES parameter to a pointer containing to a set of factors (one for each marker). Each factor should have same labels, in the same order. The linkage groups for each marker are supplied in a factor by the CHROMOSOMES parameter.

The PLOT option controls the type of graph that is displayed:

    all produces a shade plot where the genotypes are displayed using different colours, and
    missing produces a shade plot displaying the missing marker genotypes.

The LOWERGENOTYPE and UPPERGENOTYPE options can be used to display a subset of genotypes, by supplying values for the lower and upper genotypes to be included in the plot.

The DCHROMOSOMES option can be used 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 type of population must be specified using the POPULATIONTYPE option. The following settings are available:

    BC1 first generation backcross population,
    DH1 doubled-haploid population,
    F2 an F2 population,
    RIL population of recombinant inbred lines,
    BCxSy population of backcross inbred lines, and
    AMP data for association mapping.

The parent information must be supplied using the PARENTS parameter in a pointer to a set of texts. The first text in the pointer defines the alleles for parent 1, the second text defines the allele for parent 2, and so on. The labels for the parents are supplied in a text using the IDPARENTS parameter.

The COLOURS option can specify colours for the different marker scores. The colours can be supplied in a variate of RGB colours or in a text containing names of Genstat’s predefined colours (see PEN). For a plot of the marker scores, the number of colours specified by the text or variate should match the number of different marker scores for the population, while for a missing-score plot they should represent those that are present, missing and partially missing (F2, RIL and BCxSy populations). For example, for a plot of the marker scores for a DH1 population, three colours should be supplied for the scores 1/1, 2/2 and -/-. Similarly, for a missing genotype plot for a DH1 population, two colours should be supplied to represent the present and missing scores.

The TITLE option allows you to supply a title for the plot.



Action with RESTRICT

Any restrictions are ignored.

See also


Commands for: Statistical genetics and QTL estimation, Graphics.


CAPTION     'DQMKSCORES example'; STYLE=meta
QIMPORT     [POPULATIONTYPE=F2] FILENAME='%GENDIR%/Examples/F2maize_geno.txt';\
            MKSCORES=mgenotypes; CHROMOSOMES=linkagegroups;\
            PARENTS=mparents; IDPARENTS=midparents
            CHROMOSOMES=linkagegroups; PARENTS=mparents; IDPARENTS=midparents
DQMKSCORES  [PLOT=missing; POPULATIONTYPE=F2] mgenotypes;\
            CHROMOSOMES=linkagegroups; PARENTS=mparents; IDPARENTS=midparents

Updated on June 20, 2019

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