Downfreq program is used to estimate allele frequencies and eliminating missing alleles from pedigree file. Using correct allele frequencies is important since incorrect frequencies can lead to false positive findings.
Command is:
downfreq
Input files are LINKAGE formatted pedigree file (inped.dat) and locus file (indata.dat).
In following example alleles will be downcoded (1st question: y), missing alleles will be eliminated (2nd question: 1), frequencies from all individuals will be used (3rd question) and no additional alleles are chosen for each marker (last questions: n):
% downfreq
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
$$$ $$$
$$$ Program DOWNFREQ - Version 2.1 $$$
$$$ $$$
$$$ 2/11/96 $$$
$$$ $$$
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
This program estimates allele frequencies from pedigree data by
1) Allele frequencies in Founder Individuals, where typed
2) All Individuals in all pedigrees - needed to see if alleles never occur
Downcoding is also done in a rudimentary fashion by one of two simple methods:
1) Simply eliminating alleles which never occur in this pedigree material
2) Manual user-driven collapsing of alleles into allele classes
Do you wish to downcode the data (Y/n) ?
y
Do you wish to :
(1) Eliminate missing alleles or
(2) Collapse alleles into classes manually?
The first option will keep exact lod scores,
while the second will be approximate, but will
allow for much greater reduction in number of alleles.
1
Reading indata.dat
Reading inped.dat
Frequency estimates for locus 2
Allele Frequency Estimates
---------------------------------
Allele Total Founders All Individuals
1 9 0.750000 0.500000
2 3 0.250000 0.166667
3 2 0.000001 0.111111
4 0 0.000000 0.000000
5 4 0.000001 0.222222
Heterozygosity = 0.660494 Polymorphism Information Content = 0.611092
Frequency estimates for locus 3
Allele Frequency Estimates
---------------------------------
Allele Total Founders All Individuals
1 0 0.000000 0.000000
2 0 0.000000 0.000000
3 2 0.142857 0.153846
4 6 0.428571 0.461538
5 5 0.428571 0.384615
Heterozygosity = 0.615385 Polymorphism Information Content = 0.535275
Which allele frequency estimates should be used?
1 = founders; 2 = all individuals;
3 = frequencies given in original datafile
2
Originally there were 5 alleles specified at this locus.
Only 4 of them occurred in your pedigree data at least once.
Do you wish to allow for one additional allele to contain the probability
for "some other allele" at this locus? (Y/n)
n
Originally there were 5 alleles specified at this locus.
Only 3 of them occurred in your pedigree data at least once.
Do you wish to allow for one additional allele to contain the probability
for "some other allele" at this locus? (Y/n)
n
%
Downfreq prints to screen allele frequency statistics for each marker (founder and all individual frequencies), heterozygosity and polymorphism information content (=PIC). Same info is also stored to Outfile.txt. New output files are pedin.dat (pedigree file) and datain.dat (locus file), with estimated allele frequencies and downcoded alleles.