README for 'carriers'.

Sharlee Climer, November 2009.

The 'carriers' program is useful for identifying candidate multi-SNP interaction clusters, 
but can only be used when the correlated alleles are specified. It can be used on CCC 
output that used the allele network option, followed by BFS, and optionally also followed 
by a clustering routine.  

carriers considers each cluster of alleles one at a time and checks the original genotype data
to count the number of individuals that possess all of the relevant alleles.  It then 
compares these tallies for Cases and Controls and outputs clusters that are carried by at 
least one individual. 

The usage can be found by typing './carriers'  It follows:

Fatal: Usage:
  carriers clusters.bfs cases.genotypes controls.genotypes numHeadRowsGen numHeadColsGen 
snp_info.txt numColsSNPinfo numHeadRowsSNPinfo numCases numControls numSNPs outputFile.txt

The first input file 'clusters.bfs' contains the cluster memberships of each of the 
alleles.  The second input file 'cases.genotypes' contains the original Cases genotype data.
The third input file is the same for Controls.  The fourth and fifth arguments are the 
numbers of header rows and columns in the genotyped input files, respectively. The sixth
argument is the file that contains the SNP info to be printed out for each bloc. The SNPs 
must be ordered consistently for the two genotype files and the SNP info file! The 
seventh argument is the number of columns in the SNP info file and the eighth argument
is the number of header rows in the SNP info file. The ninth and tenth arguments are the 
numbers of Cases and Controls, respectively.  The eleventh argument is the number of SNPs.  
The last argument is the name of the output file.

The output file lists each of the clusters that are possessed by at least one individual, 
along with annotations. For each cluster, the cluster number, the number of nodes, and 
the number of Cases and number of Controls are stated.

The executable can be tested by typing:

./carriers small.bfs small.case.snp small.ctrl.snp 0 6 small.info.txt 5 1 10 8 5 temp.out

After running, 'temp.out' should match 'check.out'.



Please contact sharleeclimer@gmail.com with questions, suggestions, bug reports, etc.