Order Algorithm

Parameters | Genetics | Order Algorithm

Order Algorithm

Use this parameter to specify the algorithm to use for determining an initial marker order for each linkage group.

For the standard Linkage Map Order process:

Available algorithms are described in the table below:

Option

Definition

Map Order Optimization

This method uses directed graph theory with constraints on the magnitude of the recombination fraction for markers ordered next to each other. It is suitable for more complex problems, and it can be used when a framework map is specified, but it not targeted to very large data sets.

This process uses the OptModel procedure in SAS/OR

Multidimensional Scaling (MDS)

A dimension-reduction method that attempts to find the coordination of markers in one dimension that best correlations and represents the full pairwise recombination matrix.

This method is a quick solution and works well with a small number of markers in well defined linkage groups.

Accelerated Map Order Optimization

(experimental)

A more sophisticated algorithm that uses directed graph theory with constraints on the magnitude of the recombination fraction for markers ordered next to each other. This method is a more targeted algorithm that can find optimal marker orders even with very large data sets. However, it can not be used when a framework map is specified.

This process uses OptNet procedure in SAS/OR.

For the Linkage Map Order for Outcrosses process¹

Available algorithms are described in the table below:

Option

Definition

Automated

Uses the Order.seq function from OneMap R package¹. If a Framework Order Variable is specified on either of the General or Order Data Set tabs, a customized Order.seq function is used to honor the order of markers in the given framework.

RCD

Uses the rcd function from OneMap. This function implements the Rapid Chain Delineation algorithm (Doerge, 1996²).

Seriation

Uses the seriation function from OneMap. This function implements the Seriation algorithm (Buetow and Chakravarti, 1987³).

Record

Uses the record function from OneMap. This function implements the Recombination Counting and Ordering algorithm (Van Os et al., 2005⁴).

UG

Uses the ug function from OneMap. This function implements the Unidirectional Growth algorithm (Tan and Fu, 2006⁵).

Compare

Uses the compare function from OneMap.

Note: This function can be very time-demanding if there are many markers in the linkage group (more than 10 markers, for example), because this function compares all possible orders of the markers. For m markers, this function compares all m!/2 possible orders of markers.

1

Margarido, G.R.A., Souza, A.P. and Garcia, A.A.F. 2007. OneMap: software for genetic mapping in outcrossing species. Hereditas 144:78-79.

2

Doerge, R.W. 1996. Constructing genetic maps by rapid chain delineation. J. Quant. Trait Loci 2: 121-132.

3

Buetow, K.H and Chakravarti, A. 1987. Multipoint gene mapping using seriation. I. General methods. Am. J. Human Genetics 41: 180-188.

4

Van Os, H., Stam, P., Visser, R.G.F. and Van Eck, H.J. 2005. RECORD: a novel method for ordering loci on a genetic linkage map. Theor. Appl. Genet. 112: 30-40.

5

Tan, Y. and Fu, Y. 2006. A novel method for estimating linkage maps. Genetics 173: 2383-2390.

Note: When a variable is specified in the Marker Order Variable field in the Order Data Set tab, none of these algorithms are used. Instead, a map is estimated using the OneMap map function. This function estimates multipoint log-likelihood, linkage phases, and recombination ratios for a given fixed order of markers.

To Specify the Algorithm to Be Used:

Click on the appropriate radio button.

1

Note: This process is available in the Outcross Linkage Map Analysis JMP Add-In only. This Add-In is available for installation from C:\Program Files\SASHome\JMPGenomics\13\Genomics\OutCross directory or for download from the JMP File Exchange web page.

Option	Definition
Map Order Optimization	This method uses directed graph theory with constraints on the magnitude of the recombination fraction for markers ordered next to each other. It is suitable for more complex problems, and it can be used when a framework map is specified, but it not targeted to very large data sets. This process uses the OptModel procedure in SAS/OR
Multidimensional Scaling (MDS)	A dimension-reduction method that attempts to find the coordination of markers in one dimension that best correlations and represents the full pairwise recombination matrix. This method is a quick solution and works well with a small number of markers in well defined linkage groups.
Accelerated Map Order Optimization (experimental)	A more sophisticated algorithm that uses directed graph theory with constraints on the magnitude of the recombination fraction for markers ordered next to each other. This method is a more targeted algorithm that can find optimal marker orders even with very large data sets. However, it can not be used when a framework map is specified. This process uses OptNet procedure in SAS/OR.

Option	Definition
Automated	Uses the Order.seq function from OneMap R package¹. If a Framework Order Variable is specified on either of the General or Order Data Set tabs, a customized Order.seq function is used to honor the order of markers in the given framework.
RCD	Uses the rcd function from OneMap. This function implements the Rapid Chain Delineation algorithm (Doerge, 1996²).
Seriation	Uses the seriation function from OneMap. This function implements the Seriation algorithm (Buetow and Chakravarti, 1987³).
Record	Uses the record function from OneMap. This function implements the Recombination Counting and Ordering algorithm (Van Os et al., 2005⁴).
UG	Uses the ug function from OneMap. This function implements the Unidirectional Growth algorithm (Tan and Fu, 2006⁵).
Compare	Uses the compare function from OneMap. Note: This function can be very time-demanding if there are many markers in the linkage group (more than 10 markers, for example), because this function compares all possible orders of the markers. For m markers, this function compares all m!/2 possible orders of markers.