Plots a grid of marker scores for genotypes and indicates missing data (D.A. Murray).
Options
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 |
Parameters
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 |
Description
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.
Options: PLOT, LOWERGENOTYPE, UPPERGENOTYPE, DCHROMOSOMES, POPULATIONTYPE, COLOURS, TITLE
.Parameters: MKSCORES, CHROMOSOMES, PARENTS, IDPARENTS.
Action with RESTRICT
Any restrictions are ignored.
See also
Procedures: DQMAP, DQMQTLSCAN, DQSQTLSCAN, QMKDIAGNOSTICS.
Commands for: Statistical genetics and QTL estimation, Graphics.
Example
CAPTION 'DQMKSCORES example'; STYLE=meta
QIMPORT [POPULATIONTYPE=F2] FILENAME='%GENDIR%/Examples/F2maize_geno.txt';\
MAPFILENAME='%GENDIR%/Examples/F2maize_map.txt';\
MKSCORES=mgenotypes; CHROMOSOMES=linkagegroups;\
PARENTS=mparents; IDPARENTS=midparents
DQMKSCORES [PLOT=all; POPULATIONTYPE=F2] mgenotypes;\
CHROMOSOMES=linkagegroups; PARENTS=mparents; IDPARENTS=midparents
DQMKSCORES [PLOT=missing; POPULATIONTYPE=F2] mgenotypes;\
CHROMOSOMES=linkagegroups; PARENTS=mparents; IDPARENTS=midparents