silcLOD (significance levels and critical LODs) is designed to calculate nominal significance levels and critical LOD scores depending on the length of the investigated region, number of chromosomes, and the cross-over rate. The global significance level as well as the precision of the calculation have to be specified.

The program is based on the following publication:
Lander, E., Kruglyak, L. (1995) Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results.Nature Genetics, 11, 241-247.

silcLOD is started by typing "silcLOD".

Within the program, you are prompted to specify the following parameters:

• Length of genomic region in Morgan: Length of the investigated region. The default is given by 33 (length of the human genome).
• Number of chromosomes: Number of investigated chromosomes. The default is given by 23 (total number of human chromosomes).
• Cross over rate: Total crossing over rate between the genotypes. For different mapping methods, the values for humans are given below (according to Lander and Kruglyak, 1995, Table 1). The default is given by 2.
  
  
  

  Mapping method	Cross over rate
  Lod score analysis	1
  Allele sharing in sibs and half-sibs	2
  Allele sharing in grandparent-grandchildren	1
  Allele sharing in uncle-nephew	5/2
  Allele sharing in first cousin	8/3
  Allele sharing in first cousin, once removed	20/7
  Allele sharing in second cousin	16/5

• Global significance level: Desired global signficance level for the investigation. The default is given by 0.05.
• Precision: The precision sets the maximally allowed difference between the specified and the calculated global significance level. The default is given by 0.00000001.

In any stage, entering "?" gives help for specifying the parameters. The output can be saved or presented on screen only. The results render the nominal alpha for a single marker using an infinitely dense marker map as well as the critical LOD scores for single markers using an infinitely dense marker map or maps assuming distances of 10cM, 5cM, 2cM, or 1cM.

silcLOD

silcLOD - User Documentation

Copyright: Andreas Ziegler
Contact: Inke.Koenig@imbs.uni-luebeck.de