ReadmeEpistasis
Epistasis tests
Basically there are two ways how to test for epistasis using APSampler tools:
- running on all pairs of loci in the levels and genes, and
- restricting the run to the set of patterns of interest.
For both cases, the count_8_fields.pl script is used to go through the levels and genes file, and count mutual carriership and affection class membership for all possible pairwise combinations of the loci.
Further, the epistatic calculator, flinte.pl is used to compute interactions, so in both cases one may want to redirect the output of the count_8_fields.pl to a text file to be used by flinte.pl
Checking all pairs of loci
The command below will use the gene and levels files that are specified in the config, as well as the patient/control threshold levels, and call the call the 8-field counter.
perl count_8_fields.pl <name of the config file>
The program loads data in memory, so it only can be used in case the volume of genes is less the the RAM of the machine.
Checking on the restricted set of loci
Calling the following script will run the 8-field counter on the reduced set of data, i.e. only the patterns that are specified in the patterns file.
perl count_8_fields.pl <name of the config file> -pf <file with patterns>
The definition of a patterns for the parser is following: pattern is anything that ends with dot, has :, does not have spaces after :, which means that that the standard APSampler patterns can be used (locus1:allele1; locus2:allele2.).
In case the are patterns that have more than 2 loci, combinations of 2 will be output.
