Creating simulation data

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To use WinQTLCart's results graphing abilities, you need data for it to work on. If you haven't collected any data, though, you can still simulate a dataset that WinQTLCart can work with.

To create a data simulation file, select File>Simulation. This displays the Create Simulation Data series of dialogs.



Fill in the blanks for yourself, or accept the defaults.

Sample size

Trait mean

Random seed. Click the button to generate a new random seed.

Map function. Haldane (assumes no crossover interference) or Kosambi (assumes some crossover interference).

Cross Information. Select an experimental design option. You can select only one option to modify at a time. (At this time, only the three options below are available for selection.)

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B1. Backcross, with 1=parental line to which the F1 line was crossed.

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B2. Backcross, with 2=parental line to which the F1 line was crossed.

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SF. Selfed intercross line. Enter an integer indicating the generation. Limit is 2.

Translation table. Edit or add tokens you want to use for these genotype markers; you can enter any alphanumeric character(s) as a token.

Note

WinQTLCart assumes that the A allele is diagnostic for the High (parental 1) line and the a allele is diagnostic for the Low (parental 2) line. A minus sign (-) means the allele is unknown. WinQTLCart uses the numbers (2, 1, 0, 12, 10, -1) to determine how to encode the output of the genotypes. The alphanumeric tokens you enter here indicate how you have coded the markers in the source data. See the topic MCD file format for more information.

Chromosome and marker information

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Total chromosome number. The total number of chromosomes. Click the spin dial to the right of this field to select more or fewer.

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Current chromosome. Shows the active chromosome you're working on. Click the spin dial to the right of this field to select a new chromosome. You'll see the new chromosome's information in the Distance and Label boxes to the right.

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Markers for chromosome. Total number of markers for this chromosome.

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Average space between markers (cM). Produces marker positions randomly.

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Variations of the marker positions (%). How many deviations are allowed, on average

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Check Read marker positions from a text file and click Browse to select a text file containing that information. Also, select a marker distance type.

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Position. Indicates that the numbers indicate positions from the left telomere of the current chromosome. This means the numbers should be in increasing order.

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Interval. Indicates that the numbers are for the interval distance after a marker. This means that the last number, and the last number only, should be zero.

QTL numbers. Set the number of QTLs to appear in the file.
Heritability. Requires a value in the range 0.0 to 1.0. Default is 0.8.
Vd/Va. Dominant variance/Additive variance
Vi/Va. Epistatic variance/Additive variance

For the Additive, Dominant, and Epistatic effects you want to see in the simulation, you can select the following:

Effects direction

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Same—All values are positive

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Both—Values are positive and negative

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Sign's Ratio—Ratio of negative:positive.

Effects distribution

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Equal—All effects have the same value

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Normal—Values derive from normal distribution

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Gamma—Values derive from gamma distribution

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Parameter—Value for gamma distribution

Enter simulation source data filename. The file name of the MCD file that will be created.

Note	For more information on effects distribution and the additive, dominant, and epistatic effects, please refer to the QTL Cartographer's manual.

After inputting the parameters in the previous two dialogs, the final dialog presents the data simulation model you have built. Click in any cell to see that cell's values represented in the fields below.

Use the fields to edit a cell's contents. Click the Update button to write the change to the model.

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Click Save… to save your model to a .QPE (position and effects) file. The current working directory is selected as the default. (Click the X in the dialog's upper right corner to close without saving.)

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Click Load… to load a .QPE file to this window. The file's values replace the values you see in the current window.

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Click Adjustment to adjust values for the entire genome.

Click OK to produce the simulation data file. You can then use that file for analysis.

Related topics
Showing QTL information