VI - The trait selection menu

The trait selection menu allows the user to select one or more traits and place them before or after the marker loci inside the output files. Some analysis options allow only a single traits locus at a time, in which case the third option is not available. In other cases, only affection status loci are allowed, and the trait selection process will not terminate unless a valid set of traits have been chosen. (See More details on trait selection for specific analysis options.) 

Trait and covariate selection menu:
0) Done with this menu - please proceed.
 1) Trait loci selected: [d1 d2 [MARKERS]]
 2) Create trait-specific files or combine: [Combine]


1) List of selected trait loci:

Option 1 allows to user to specify zero or more trait loci to be used in the analysis. If there is only a single trait locus, and the analysis option requires at least one trait locus, then this menu is skipped, and the trait locus automatically selected. For these options, if no trait loci are present, or the trait locus is not of the correct type (e.g. SimWalk2-NPL requires at least one affection locus, and the data has only QTLs), then Mega2 will stop with an error message.
If option 2 is set to "one locus at a time", a list of trait loci are displayed, and the user enters 0 or more corresponding numbers. If option 2 is set to "combine", then the trait list also includes a [MARKER] item. In this case the order of the loci decides the order in which they appear in the output files.

2) Select multiple trait loci to loop across.

If Option 2 is set to "one trait at a time", the analysis is carried out with one trait and all marker loci at a time. The output for each trait is stored in a sub-directory (see Output directory selection menu). Trait loci are selected via option 1, and the order in which they are selected does not affect the output, except the order in which each trait is analyzed. to the traits.

3) Use trait loci in specified order.

If Option 2 is set to "combine", then all traits are combined into a single set of output files. Trait loci appear in the output files in the order they are selected in. Choosing this option also allows trait loci to be placed before and after the marker loci.

4) More details on trait selection.

The following options require at least one affection status trait locus:

Simwalk2: Parametric (Location scores) and Non-parametric linkage
Aspex
GeneHunter, GeneHunter-Plus, Allegro, and MLBQTL
APM and APM-Mult
SPLINK
Segregation and liability group counts
TDTMax
Vitesse

The following do not allow quantitative trait loci:

Simwalk2 options
Aspex
GeneHunter-Plus and Allegro
APM and APM-Mult
SIMULATE
Segregation and liability group counts
TDTMax

The following options can handle quantitative trait loci but require at least one affection status locus. For these options if the user doesn't specify an affection status locus, a dummy locus is inserted in the output files.

GeneHunter
MLBQTL

VI - The covariate selection item

This menu allows the selection of covariates and appears only if the data includes QTLs and the Genehunter option is selected. We will include more options such as Merlin, SOLAR etc. in the future to make use of this feature.
Here is what the trait menu looks like with the covariates item: 


Trait and covariate selection menu:
0) Done with this menu - please proceed.
 1) Trait loci selected: [Q1]
 2) Covariates selected: []
 3) Loop over traits or combine traits: [Loop   ]
Enter option 0 - 3 >

Traits appearing in the list in option 1 is automatically excluded from the list of covariates.