Calcsim2.sh is a script which is used for power simulations by using SLINK.
Command is:
calcsim2.sh
Input files are:
Datafile (simdata.dat)
Create datafile by using makedata (or preplink) program with one disease loci and one marker loci. Marker loci have to have 4 alleles and allele set frequences for each allele 0.25.
Makedata steps:
Use your own disease model, not which are in this example!
Makedata 1.4 (06/17/1999). This program creates data files for linkage
analysis. Maxlocus 60. Made by Tero Juntunen
How many marker loci?
1
Is this set of markers?
(1) Autosomal
(2) Sexlinked
1
What is the assumed frequecy of the disease allele?
0.001
How many liability classes?
1
Please enter penetrances for liability class 1.
P(Aff|DD) P(Aff|D+) P(Aff|++)
1.0 1.0 0
What is the largest number of alleles at any markers?
4
Do you want to specify recombination fraction between markers?
(0=No, 1=Yes, 2=AUTOSCAN option)
0
Indata.dat created! Run downfreq to eliminate alleles
and calculate correct allele frequences.
Now edit indata.dat file and change second last line:
0.00 if you have candidate gene model
0.05 genomescan model
Save file as simdata.dat
Pedigree file (simpre.dat)
Pedigree file is pre-makeped format linkage pedigree file and columns are:
Column 1: Pedigree identifier { The identifier can be a number
Column 2: Individual's ID { or a character string
Column 3: The individual's father { If the person is a founder, just put a
Column 4: The individual's mother { 0 in each column.
Column 5: Sex { 1 = Male, 2 = Female, Unknown sex is not permitted
Column 6: Affection status { Disease and marker phenotypes
Column 7: 0 { See Terwilliger JD & Ott J (1994) for details
Column 8: 0 { See Terwilliger JD & Ott J (1994) for details
Column 9: 0 or 2 { set this column to 2 if you have DNA (e.g. typed)
or 0 if you don't have DNA (e.g. untyped)
Save file as simpre.dat
slinkin.dat
Line 1: random seed
Line 2: number of replicates
Line 3: locus number of trait locus
Line 4: the proportion of unlinked families
Example:
26710
100
1
0
limit.dat
1 2 3
See Terwilliger JD & Ott J (1994) for details.
Finally execute calcsim2.sh.
See results from msim.dat
Script by Tero Hiekkalinna
Page 254: Handbook of Human Genetic Linkage, Joseph D. Terwilliger and Jurg Ott. Johns Hopkins University Press, Baltimore (1994)