A toy example of analysis:
To fit the variance component model, you need to specify the input data (-d parameter), pedigree (-p parameter) and map (-m parameter) files and the --vc option. Other related options include --start (start position for analysis), --stop (stop position for analysis) and --grid (the distance between grid points in the unit of Mb. LOD score at each grid point will be output).
prompt> merlin -d LDL.dat -p LDL.ped -m LDL.map --vc
After running the command, you should see the MERLIN banner and a summary of currently selected options:
MERLIN LOCAL - (c) 2000-2007 Goncalo AbecasisReferences for this version of Merlin: Abecasis et al (2002) Nat Gen 30:97-101 [original citation] Fingerlin et al (2004) AJHG 74:432-43 [case selection for association studies] Abecasis and Wigginton (2005) AJHG 77:754-67 [ld modeling, parametric analyses] Fingerlin et al (2006) Gen Epidemiol 30:384-96 [sex-specific maps] Chen and Abecasis (2007) AJHG 81:913-26 [qtl association analysis, qtl simulation]
The following parameters are in effect: Data File : LDL.dat (-dname) Pedigree File : LDL.ped (-pname) Missing Value Code : -99.999 (-xname) Map File : LDL.map (-mname) Allele Frequencies : ALL INDIVIDUALS (-f[a|e|f|m|file]) Random Seed : 123456 (-r9999) Data Analysis Options General : --information, --likelihood, --model [param.tbl] Errors : --flag, --perAllele [0.00], --perGenotype [0.00], --fit IBD States : --ibd, --kinship, --matrices, --extended, --select NPL Linkage : --npl, --pairs, --qtl, --deviates, --extras, --exp VC Linkage : --vc [ON], --useCovariates, --ascertainment, --unlinked [0.00] Association : --infer, --assoc, --fastAssoc, --filter, --custom [cov.tbl] Haplotyping : --best, --sample, --all, --founders, --horizontal Recombination : --zero, --one, --two, --three, --singlepoint Positions : --steps, --maxStep, --minStep, --grid [], --start [], --stop [] LD Clusters : --clusters [], --distance, --rsq, --cfreq Limits : --bits [24], --megabytes, --minutes Performance : --trim, --noCoupleBits, --swap, --smallSwap, --cache [] Output : --quiet, --markerNames, --frequencies, --perFamily, --pdf, --tabulate, --prefix [merlin] Simulation : --simulate, --reruns, --save, --trait [] Estimating allele frequencies... [using all genotypes] MRK
After a few moments, you should see analysis results at each location:
Information on repeated measurements found An average of 5.5 measurements per subject were taken A measurement error component will be fitted
Phenotype: simp_phen [VC] (1000 families, h2 = 37.96%, error = 40.42%) ================================================================== Position H2 ChiSq LOD pvalue 0.000 9.88% 15.35 3.33 0.00004
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