FLOSS version 1.4.1
java -jar floss.jar -c test.cov -merlin merlin.lod -o floss.test --npl
The following parameters are in effect:
Score Statistic: NPL z-score using S_all (--npl)
Score Filename: merlin.lod (-merlin name)
Covariate File: test.cov (-c name)
Output Prefix: floss.test (-o prefix)
Subset Type: extreme (-subsets type)
Random Seed: 0 (-seed integer)
Min Permutations: 100 (-minperm integer)
Max Permutations: 10000 (-maxperm integer)
Covariates in order of analysis:
1) cov1.Avg1All
2) cov2.Avg1All
3) cov3.Avg1All
4) cov4.Avg1All
5) cov5.Avg1All
6) cov6.Avg1All
Maximum Linkage Score with all (47) families: 0.58 at locus 20.000
Brief Summary
--------------------------------------------------------------------------------
New Old Delta
Covariate Peak Max Max Max p-value #Families
--------------------------------------------------------------------------------
1) cov1.Avg1All 16.000 2.87 0.58 2.29 0.128 -2/47
2) cov2.Avg1All 32.000 1.61 0.80 0.81 0.931 -29/43
3) cov3.Avg1All 68.000 1.97 0.58 1.38 0.554 -7/47
4) cov4.Avg1All 60.000 1.89 0.58 1.30 0.673 -2/47
5) cov5.Avg1All 68.000 1.84 0.80 1.04 0.822 -24/43
6) cov6.Avg1All 68.000 2.37 0.80 1.57 0.416 -14/43
Ordered Subset Summary
--------------------------------------------------------------------------------
First Last Best Total
Covariate Family Family Cov Range Cov Range
--------------------------------------------------------------------------------
1) cov1.Avg1All 7 11 [22.0, 23.9] [22.0, 49.0]
2) cov2.Avg1All 38 15 [79.6, 167] [79.6, 253]
3) cov3.Avg1All 31 18 [87.0, 108] [87.0, 238]
4) cov4.Avg1All 1 17 [3.13, 3.29] [3.13, 24.5]
5) cov5.Avg1All 31 41 [87.0, 102] [87.0, 151]
6) cov6.Avg1All 1 18 [3.27, 6.98] [3.27, 25.9]
Permutation Test Summary
--------------------------------------------------------------------------------
Covariate Success Perms p-value 95% Conf Int
--------------------------------------------------------------------------------
1) cov1.Avg1All 20 156 0.128 [0.0820, 0.193]
2) cov2.Avg1All 93 100 0.931 [0.856, 0.969]
3) cov3.Avg1All 55 100 0.554 [0.448, 0.649]
4) cov4.Avg1All 67 100 0.673 [0.568, 0.759]
5) cov5.Avg1All 82 100 0.822 [0.728, 0.887]
6) cov6.Avg1All 41 100 0.416 [0.314, 0.513]
DOCUMENTATION
Brief Summary:
==============
Covariate = name of covariate as given in the Covariate file. The covariate
name typically has the format [name].[extension] where [extension]
identifies how the family covariate score was calculated
Peak (cM) = location of maximum score, maximized over all ordered subsets.
New Max = maximum score, maximized over all loci and ordered subsets.
Old Max = maximum score using all families with a covariate value,
maximized over all loci.
Delta Max = (New Max) - (Old Max).
p-value = probability of observing a change in LOD score greater than or
equal to Delta Max if family linkage scores and family covariate
scores are independent.
#Families = [# in best ordered subset] / [# with defined covariate values]
An initial + or - means the best ordered subset consists of
families with the highest (+) or lowest (-) covariate scores.
Ordered Subset Summary:
=======================
Covariate = name of covariate -- see description above (in Brief Summary).
First Family = identifier of family with smallest covariate score in the
ordered subset with highest linkage score.
Last Family = identifier of family with largest covariate score in the
ordered subset with highest linkage score.
Best Cov Range = range of covariate values in the ordered subset with highest
linkage score.
Total Cov Range = range of covariate scores in the set of all families.
Permutation Test Summary:
=========================
Covariate = name of covariate -- see description above (in Brief Summary).
Success = number of permutations with an ordered subset score greater than
or equal to the maximum ordered subset score obtained when
ordering by the family covariate values.
Perms = number of permutations.
p-value = see description above (in Brief Summary).
95% Conf Int = 95% confidence interval for the estimated p-value.