Analyze performs parametric linkage analysis (MLINK), nonparametric affected sib-pair analysis (ASP), family-based association analysis (TDT, HRRR), and homogeneity testing (HOMOG).
Input files are LINKAGE formatted pedigree (pedin.dat) and locus (datain.dat) files.
To set up analysis, run first analprep program
analprep
It will ask following questions:
Respond to the following queries with (0 = no) or (1 = yes):
Do you want parametric linkage analysis?
Do you want disequilibrium analysis with HHRR?
Do you want sibpair analysis?
Do you want linkage analysis with TDT?
Do you want linkage analysis on component nuclear pedigrees?
Do you want polylocus linkage analysis - requires locus order?
Do you want multipoint HHRR analysis - requires locus order?
Analprep command creates analyze named Unix shell script which can be run after that with command:
sh analyze
Summary of analysis is in summary.out (example here) and more detail info is in analyze.final (example here).
Kuokkanen S, Sundvall M, Terwilliger JD, Tienari PJ, Wikstrom J, Holmdahl R, Pettersson U, Peltonen L. A putative vulnerability locus to multiple sclerosis maps to 5p14-p12 in a region syntenic to the murine locus Eae2. Nat Genet 1996 Aug;13(4):477-80
SIBPAIR:Kuokkanen S, Sundvall M, Terwilliger JD, Tienari PJ, Wikstrom J, Holmdahl R, Pettersson U, Peltonen L. A putative vulnerability locus to multiple sclerosis maps to 5p14-p12 in a region syntenic to the murine locus Eae2. Nat Genet 1996 Aug;13(4):477-80
TDT (statistics based on an algorithm of):Terwilliger JD, A powerful likelihood method for the analysis of linkage disequilibrium between trait loci and one or more polymorphic marker loci. Am J Hum Genet 1995 Mar;56(3):777-87
HHRR:Terwilliger JD, A powerful likelihood method for the analysis of linkage disequilibrium between trait loci and one or more polymorphic marker loci. Am J Hum Genet 1995 Mar;56(3):777-87
HOMOGOtt J (1986) Linkage probability and its approximate confidence interval under possible heterogeneity. Genet Epidemiol Suppl 1:251-257
FASTLINK 4.1P:R. W. Cottingham Jr., R. M. Idury, and A. A. Schaffer, Faster Sequential Genetic Linkage Computations, American Journal of Human Genetics, 53(1993), pp. 252-263.
and
A. A. Schaffer, S. K. Gupta, K. Shriram, and R. W. Cottingham, Jr., Avoiding Recomputation in Linkage Analysis, Human Heredity, 44(1994), pp. 225-237.