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.