This file illustrates how to use preplink. To start, type: preplink
The first menu looks like:
=============PRESENT STATUS===============
(a) Number of loci : 2
(b) Sexlinked : N
(c) Calculate Risk : N
(d) Mutation : N
(e) Haplotype frequencies : N
(f) Locus Order : 1 2
(g) Interference : N
(h) Recombination sex difference : N
(i) Program used : MLINK
(j) Recombination values :
0.100
==============OTHER OPTIONS===============
(k) See or modify loci discription [sic]
(l) See or modify recombination to vary
(m) Read datafile
(n) Write datafile
(o) Exit
==========================================
Enter letter to modify or see values
Default values are shown. All of these values can be modified. Item i is mostly irrelevant, unless you want to do a special computation such as risk calculation. Item j is irrelevant because theta is chosen in lcp.
Item k is the basic operation to enter loci. Entering k, you will see:
------------------------------------------ (1) binary factors GENE FREQS : 0.500000 0.500000 (2) binary factors GENE FREQS : 0.500000 0.500000 ------------------------------------------ (a) SEE OR MODIFY A LOCUS (b) DELETE LOCUS (c) ADD LOCUS (d) CHANGE ORDER TO CORRESPOND TO PEDIGREE FILE (NOT CHROMOSOME ORDER) (e) CHANGE LOCUS TYPE (f) RETURN TO MAIN MENU ------------------------------------------ enter letter to modify values
This shows the default settings for loci. It is unfortunate that the default
type of locus is "binary factors", because this is almost useless. Let's
change the first locus to be of the "affection status" flavor.
Entering e, what comes back is:
ENTER LOCUS TO CHANGE
Enter 1, and get back:
ENTER NEW LOCUS TYPE: (a) BINARY FACTORS (b) QUANTITATIVE TRAIT (c) AFFECTION STATUS (d) ALLELE NUMBERS
Enter c, and get back:
------------------------------------------ (1) affection status GENE FREQS : 0.500000 0.500000 (2) binary factors GENE FREQS : 0.500000 0.500000 ------------------------------------------ (a) SEE OR MODIFY A LOCUS (b) DELETE LOCUS (c) ADD LOCUS (d) CHANGE ORDER TO CORRESPOND TO PEDIGREE FILE (NOT CHROMOSOME ORDER) (e) CHANGE LOCUS TYPE (f) RETURN TO MAIN MENU ------------------------------------------ enter letter to modify values
Enter a and then 1 to change locus 1. After those two steps, you will see:
LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL LOCUS NUMBER : 1 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL (a) NUMBER OF ALLELES : 2 (b) NUMBER OF LIABILITY CLASSES : 1 (c) PENETRANCES : GENOTYPE 1 1 0.00000000000000e+00 GENOTYPE 1 2 0.00000000000000e+00 GENOTYPE 2 2 1.00000000000000e+00 (d) GENE FREQUENCIES : 0.500000 0.500000 (e) EXIT LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL enter letter to modify values
11 is dd, 12 is Dd, and 22 is DD by convention. CLAP is dominant,
so one must change the penetrance of the 12 genotype to be 1.0.
So enter c, and get back:
ENTER NEW PENETRANCES GENOTYPE 1 1 OLD PEN 0.00000000000000e+00 ?
You must re-enter all the penetrances, even though you want to change only one. After re-entering the 3 penetrances (one per line, enter 0, 1, and 1) you will see:
LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL LOCUS NUMBER : 1 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL (a) NUMBER OF ALLELES : 2 (b) NUMBER OF LIABILITY CLASSES : 1 (c) PENETRANCES : GENOTYPE 1 1 0.00000000000000e+00 GENOTYPE 1 2 1.00000000000000e+00 GENOTYPE 2 2 1.00000000000000e+00 (d) GENE FREQUENCIES : 0.500000 0.500000 (e) EXIT LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL enter letter to modify values
CLAP is a common disease, but the frequency of 0.5 for the disease allele is probably too high. Enter d to change the frequencies. Then get:
ENTER 2 NEW GENE FREQUENCIES
Enter: 0.99 0.01
Notes: 0.01 is an extremely high frequency for a disease allele. Typically,
users use 0.0001 or lower. preplink does not enforce that frequencies add
to 1. lsp will give a warning if frequencies sum to < 0.95 or
> 1.05.
Starting with version 3.0P, FASTLINK gives a warning unless the frequency
sum is very close to 1. The next screen is:
LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL LOCUS NUMBER : 1 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL (a) NUMBER OF ALLELES : 2 (b) NUMBER OF LIABILITY CLASSES : 1 (c) PENETRANCES : GENOTYPE 1 1 0.00000000000000e+00 GENOTYPE 1 2 1.00000000000000e+00 GENOTYPE 2 2 1.00000000000000e+00 (d) GENE FREQUENCIES : 0.990000 0.010000 (e) EXIT LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL enter letter to modify values
We are done with locus 1, so enter e to go on to another locus.
Next, you need to change locus 2, so that it uses allele numbers instead of
binary factors, has 3 alleles instead of 2, and change the allele
frequencies.
Very important: The locus type must be changed first. Then
the number and frequencies of alleles can be changed. This is because the
locus-specific menus depend on the locus type.
------------------------------------------ (1) affection status GENE FREQS : 0.990000 0.010000 (2) binary factors GENE FREQS : 0.500000 0.500000 ------------------------------------------ (a) SEE OR MODIFY A LOCUS (b) DELETE LOCUS (c) ADD LOCUS (d) CHANGE ORDER TO CORRESPOND TO PEDIGREE FILE (NOT CHROMOSOME ORDER) (e) CHANGE LOCUS TYPE (f) RETURN TO MAIN MENU ------------------------------------------ enter letter to modify values
Enter e, and then 2 to the next prompt. Then:
ENTER NEW LOCUS TYPE: (a) BINARY FACTORS (b) QUANTITATIVE TRAIT (c) AFFECTION STATUS (d) ALLELE NUMBERS
Enter d and get:
------------------------------------------ (1) affection status GENE FREQS : 0.990000 0.010000 (2) allele numbers GENE FREQS : 0.500000 0.500000 ------------------------------------------ (a) SEE OR MODIFY A LOCUS (b) DELETE LOCUS (c) ADD LOCUS (d) CHANGE ORDER TO CORRESPOND TO PEDIGREE FILE (NOT CHROMOSOME ORDER) (e) CHANGE LOCUS TYPE (f) RETURN TO MAIN MENU ------------------------------------------ enter letter to modify values
Enter a and then 2 and get:
aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa LOCUS NUMBER : 2 aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (a) NUMBER OF ALLELES : 2 (b) GENE FREQUENCIES : 0.500000 0.500000 (c) EXIT aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa enter letter to modify values
Enter a first to modify the number of alleles. Then:
ENTER NUMBER OF ALLELES
Enter 3 and get:
(note that preplink has automatically inserted a third frequency, but
the value of 0.0 will actually cause an error in lsp, if it is not changed.)
aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa LOCUS NUMBER : 2 aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (a) NUMBER OF ALLELES : 3 (b) GENE FREQUENCIES : 0.500000 0.500000 0.000000 (c) EXIT aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa enter letter to modify values
Enter b and get:
ENTER 3 NEW GENE FREQUENCIES
Enter 3 numbers (0.6 0.3 0.1) and get:
aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa LOCUS NUMBER : 2 aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (a) NUMBER OF ALLELES : 3 (b) GENE FREQUENCIES : 0.600000 0.300000 0.100000 (c) EXIT aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa enter letter to modify values
Now we are done with locus 2. Let's add one more locus, so that
we can do multi-locus analysis. Enter c to exit the current menu
and c at the next menu to add a locus:
Notice that again the default locus type is binary factors (yuck!)
------------------------------------------ (1) affection status GENE FREQS : 0.990000 0.010000 (2) allele numbers GENE FREQS : 0.600000 0.300000 0.100000 (3) binary factors GENE FREQS : 0.500000 0.500000 ------------------------------------------ (a) SEE OR MODIFY A LOCUS (b) DELETE LOCUS (c) ADD LOCUS (d) CHANGE ORDER TO CORRESPOND TO PEDIGREE FILE (NOT CHROMOSOME ORDER) (e) CHANGE LOCUS TYPE (f) RETURN TO MAIN MENU ------------------------------------------ enter letter to modify values
Using similar keystrokes to those for locus 2, change the type and allele frequencies of locus 3 to 0.8 and 0.2. After these changes:
------------------------------------------ (1) affection status GENE FREQS : 0.990000 0.010000 (2) allele numbers GENE FREQS : 0.600000 0.300000 0.100000 (3) allele numbers GENE FREQS : 0.800000 0.200000 ------------------------------------------ (a) SEE OR MODIFY A LOCUS (b) DELETE LOCUS (c) ADD LOCUS (d) CHANGE ORDER TO CORRESPOND TO PEDIGREE FILE (NOT CHROMOSOME ORDER) (e) CHANGE LOCUS TYPE (f) RETURN TO MAIN MENU ------------------------------------------ enter letter to modify values
Now choose f to return to the main menu to finish preplink.
The main menu is:
=============PRESENT STATUS===============
(a) Number of loci : 3
(b) Sexlinked : N
(c) Calculate Risk : N
(d) Mutation : N
(e) Haplotype frequencies : N
(f) Locus Order : 1 2 3
(g) Interference : N
(h) Recombination sex difference : N
(i) Program used : MLINK
(j) Recombination values :
0.100 0.100
==============OTHER OPTIONS===============
(k) See or modify loci discription [sic]
(l) See or modify recombination to vary
(m) Read datafile
(n) Write datafile
(o) Exit
==========================================
Enter letter to modify or see values
Choose n to write the data file, enter the file name
datain.dat, and then o to exit.
The output is in the file datain.dat and it is nicely annotated
by preplink.
Here is what datain.dat looks like. The last line is irrelevant.
3 0 0 5 << NO. OF LOCI, RISK LOCUS, SEXLINKED (IF 1) PROGRAM 0 0.0 0.0 0 << MUT LOCUS, MUT RATE, HAPLOTYPE FREQUENCIES (IF 1) 1 2 3 1 2 << AFFECTION, NO. OF ALLELES 0.990000 0.010000 << GENE FREQUENCIES 1 << NO. OF LIABILITY CLASSES 0.0000 1.0000 1.0000 << PENETRANCES 3 3 << ALLELE NUMBERS, NO. OF ALLELES 0.600000 0.300000 0.100000 << GENE FREQUENCIES 3 2 << ALLELE NUMBERS, NO. OF ALLELES 0.800000 0.200000 << GENE FREQUENCIES 0 0 << SEX DIFFERENCE, INTERFERENCE (IF 1 OR 2) 0.10000 0.10000 << RECOMBINATION VALUES 1 0.10000 0.45000 << REC VARIED, INCREMENT, FINISHING VALUE
Important things to notice:
The first number is the number of loci(3).
The order of loci is on the third row.
The first number of each locus is the type of locus, so 1 means "affection
status" and 3 means "allele numbers".