Fast Mapping

The code is provided under the GNU public license (http://www.gnu.org/copyleft/gpl.html#TOC1).

Fast mapping has two parts:
1. Automatic grouping and ordering. 
2. Visualizing the data

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RUNNING FAST MAPPING

1) Drag the .loc file to be mapped onto the Fast Mapping executable

A new file named "file-name_map.loc" will be created in the same directory as the initial loc file. This results is also a .loc-formatted file.


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EXPLANATIONS FOR SUPPORTING FILES AND ARGUMENTS

Supporting files
A)
matrix.txt - The penalty scoring matrix for different alleles. Used for ordering the markers in the linkage groups.

B)
parameters.txt - parameters that need to be set to run Fast Mapping.
Description of the parameters by line:
	1)matrix file: The name of the matrix file, default is "matrix.txt"
	2)chromosomes: the presumed number of linkage groups or independent regions in the data. The program uses this parameter in the grouping step.
	3) maximum LOD for core grouping: The initial LOD_threshold for markers to be in the same group. This number is the start LOD for grouping. Later the program uses successively lower threshold to place outlying markers.
	4) minimum LOD for grouping: the LOD threshold for grouping used in the last step of grouping
	5) missing value screening ratio: the proportion from 1 to 0 for missing values in a marker above which the marker is rejected 
	6) 1 : 1 segregation chi_square threshold value: markers with a chi-square value distorted from the expected Mendelian 1 : 1 ration are rejected. The larger the number the less strict.
	7) 1 : 2 : 1 segregation chi_square threshold value: as in 6 for 1:2:1 ratio
	8) 1 : 3 segregation chi_square threshold value: as in 6 for 1:3 ratio
	9) order plants: tells Fast Mapping to order the individuals using RECORD, 1 to order, 2 to not order

B)
fast_mapping_log.txt - a log file describing the previous run of Fast Mapping


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VISUALIZING THE DATA

1) Open the Excel file provided called "with_macro.xls". You can use any Excel file but you must load the macro into it. If Excel asks you to allow macros, select "Enable Macros".
2) Go to the menu and select Tools->Macro->Macros. A menu of macros will appear, select LoadLoc. 
3) A window will pop up asking for the name of a .loc file to load, enter the name of the .loc file. 
Click OK
->The file will then load colored in excel.


Description of the .loc file loaded into Excel:

A) Columns
Column A: marker name
Last four columns:
1) spacer (;)
2) 2)recombination rate (r) 
3) LOD score for recombination (LOD),
4) distance in centimorgan acording to Kosambi (dist)
The values in the last three comlumns are related to the marker in the same row and the marker below it.

B) Rows
Rows 1-4: header of the original .loc file
Rows 8-9: Final LOD for grouping
Row 10: the position of the individual in the original .loc file. Individuals can be arranged if order plants was toggled for Fast mapping in the parameters file.
Rows 11 and on: marker genotypes