Output Details

6.2.2 Output Details

Next we will discuss the output in detail to the standard output, in the case where details = YES, checkit = NO with finite number of burn-in and follow-on iterations. This output can be redirected to a file for easier viewing.

 

  • Input parameter file name
  • Values of all the parameters specified in this file
  • Genetic distance for all chromosomes:
  • Total genomic distance
  • Count of individuals, cases, controls and ignores used in the analysis; and also the number of real and fake markers

parameter file: param2

output: outscore.dat

### THE INPUT PARAMETERS

PARAMETER NAME: VALUE

risk: 1.5

indivname: indiv1.dat

snpname: snpcnts

genotypename: geno.dat

badsnpname: badsnps

OUTD: outfiles

tlreest: YES

seed: 1011

splittau: YES

fancyxtheta: YES

checkit: NO

details: YES

output: outscore.dat

numburn: 50

numiters: 100

emiter: 30

dotoysim: NO

cleaninit: YES

reestiter: 5

thetafilename: outfiles/theta.out

lambdafilename: outfiles/lambda.out

freqfilename: outfiles/freq.out

indivoutname: outfiles/ind.out

snpoutname: outfiles/snp.out

ethnicfilename: outfiles/ethnic.out

hiclip: 100

## ANCESTRYMAP version: 6210

 

###GENETIC DISTANCE FOR ALL CHROMOSOMES

##Chr_Num: chromosome num, First_SNP and Last_SNP: First and last markers, Gen_dist: Genetic distance

Chr_Num First_SNP  Last_SNP  Gen_dist

chrom:     1  first:     0  last:  429 distance:     2.834

chrom:     2  first:   430  last:  831 distance:     2.643

chrom:     3  first:   832  last:  1163 distance:     2.227

chrom:     4  first:  1164  last:  1481 distance:     2.131

chrom:     5  first:  1482  last:  1787 distance:     2.012

chrom:     6  first:  1788  last:  2071 distance:     1.914

chrom:     7  first:  2072  last:  2360 distance:     1.871

chrom:     8  first:  2361  last:  2619 distance:     1.670

chrom:     9  first:  2620  last:  2872 distance:     1.777

chrom:    10  first:  2873  last:  3141 distance:     1.809

chrom:    11  first:  3142  last:  3381 distance:     1.552

chrom:    12  first:  3382  last:  3638 distance:     1.723

chrom:    13  first:  3639  last:  3829 distance:     1.258

chrom:    14  first:  3830  last:  4006 distance:     1.159

chrom:    15  first:  4007  last:  4189 distance:     1.245

chrom:    16  first:  4190  last:  4382 distance:     1.340

chrom:    17  first:  4383  last:  4565 distance:     1.266

chrom:    18  first:  4566  last:  4738 distance:     1.160

chrom:    19  first:  4739  last:  4895 distance:     1.069

chrom:    20  first:  4896  last:  5051 distance:     1.067

chrom:    21  first:  5052  last:  5139 distance:     0.604

chrom:    22  first:  5140  last:  5244 distance:     0.710

chrom:    23  first:  5245  last:  5426 distance:     1.180

total distance:    36.224

calling setstatus

 

emiter: 30

reestiter: 5

###COUNTS

Num of fake Markers: 3622  Num of real Markers: 1805 Spacing between fake markers:     0.010

Num of Markers: 5427   Num of Samples:  1201

Num of Cases:  600 Num of Controls:  600   Num of Ignored Samples: 1

  • Score generated for each iteration by the expectation maximization algorithm. One should observe the score increasing with the number of iterations.
  • Results of the Markov Chain Monte Carlo iterations, which include estimation of θ and l. Note that the iteration number goes from 1 –numburn to 0 for the burn-in iterations and from 1 to numiters for the follow-on iterations. Also the score is zero for the burn-in iterations, since we calculate it only for the follow-on iterations. The format of the output for the estimation of θ and l is as follows:
    estglob theta   iter   a1   b1   a2   b2   c2
    estglob lambda   iter   p1    lambda1   p2   lambda2   lambdave
    The above parameters are "global parameters" (affect every individual).  See supplementary note 2 of the Patterson et. al. 2004 paper for definitions.
    lambdaave is the average λ across individuals.

The format of the output which begins with bigiter is as follows:

bigiter   iter    ylike    LOD sc.   tau(A)    tau(E)     thetaave    lambdaave    xtave(M)   xlave(M)    xtave(F)   xlave(F)
 ylike is the slowly mixing statistic of little intrinsic interest described in the above mentioned supplementary note. xtave(M) and xtave(F) are the average θ on X chromosme for males and females respectively, xlave(M) and xlave(F) are the average l on X chromosome for males and females respectively.

  • Posterior estimates for the mean and standard deviation of θ, θX, λ, λX and t(Afr), t(Eur). The user should look at the values of t(African) and t(European) carefully, since these are an indicator of how well the ancestral models fit the data. It is worrisome if these values are less than 100.
  • Genome-wide scores for all the models

##SCORES FROM EXPECTATION_MAXIMIZATION ALGORITHM ITERATIONS

##         Iteration_Num    Score

emsimple iter:      1          0.000

emsimple iter:      2      78381.771

emsimple iter:      3     100906.993

emsimple iter:      4     108153.527

 

 

emsimple iter:     29     113979.572

emsimple iter:     30     114004.635

muval1:     0.000

neil0:     5.927    -3.414

domcm1 time:    25.150

 

##RESULTS FOR EACH MARKOV CHAIN MONTE CARLO ITERATION

##estglob theta: Iteration_Num  thp1  thp2  thxp0  thxp1  thxp2

##thp1, thp2: Are parameters for the prior distribution of theta, and thxp0,thxp1,thxp2 are the same for theta on X chromosome

##estglob lambda: Iteration_Num  lp1  lp2  lxp1  lxp2  ave_lambda

##lp1, lp2: Are parameters for the prior distribution of lambda, and lxp1,lxp2 are the same for lambda on X chromosome

 

estglob theta    -49     1.894     7.204       1.054     9.168    40.026

estglob lambda   -49    13.857     2.725      10.599     2.063     5.086

domcm1 time:    25.170

estglob theta    -48     2.024     7.845       1.147     9.027    37.570

estglob lambda   -48    16.798     3.267      10.370     2.029     5.141

 

 

estglob theta     98     2.080     8.646       2.372    12.278    51.136

estglob lambda    98    16.088     2.691       9.548     2.171     5.963

estglob theta     99     2.065     8.454       2.389    11.843    53.460

estglob lambda    99    18.687     3.146       9.201     2.041     5.985

estglob theta    100     2.005     7.963       2.270    12.302    51.769

estglob lambda   100    16.885     2.828       9.888     2.216     5.973

average thetax:   229.264

 

###POSTERIOR ESTIMATES

theta  mean      0.1986

thetax mean      0.1911

theta  var      0.0141   sdev:     0.1189

thetax var      0.0124   sdev:     0.1114

 

lambda  mean      5.9800

lambdax mean      4.5341

lambda  var      1.9976   sdev:     1.4134

lambdax var     23.0519   sdev:     4.8012

tau (PopA)   108.270

tau (PopB)   114.625

 

 

###GENOME_WIDE SCORE FOR ALL THE MODELS

##risk1 and risk2 are the increased risk due to having one or two population A ancestry alleles, and  crisk: risk for controls

           risk1     risk2     crisk       score

model:     1.500     2.250     1.000      13.633

  • θ/M and λ values for all individuals
  • Allele frequency estimates with standard error:
  • Lag and correlations
    For a number of sample statistics we compute a correlation coefficient at small "lags". If the statistic at iteration i is S(i) we compute  for 1 <= lag <= 10 (default) the correlation between S(i) and S(i+lag). Large values indicate that the MCMC is not mixing very well.
    We publish this for:
    • llike:  a statistic of no intrinsic interest but mixes poorly.    
    • log10fac:  Log_10 Bayes factor (genome wide)
    • factor: Bayes factor = 10^log10fac
    • log tauscal: log (t(0)) the t value for population 0.

In our experience ii), iii) are the most important statistics which mix well, iv) mixes less well and i) mixes quite poorly.

###THETA or M, LAMBDA VALUES FOR ALL INDIVIDUALS

##Indiv_Index: individual's internal index num, tmean and txmean: average theta and thetax

##tsdev and txsdev: standard deviation for theta and thetax

##lmean and lxmean: average lambda and lambdax

##lsdev and lxsdev: standard deviation for lambda and lambdax

 Num        Indiv_ID Gender    tmean     tsdev     txmean    txsdev        lmean     lsdev     lxmean    lxsdev

 

   0                toyindiv:0     M     0.214     0.028      0.206     0.063        5.470     0.750      5.156     1.469

   1                toyindiv:1     F     0.112     0.016      0.127     0.042        7.202     0.705      4.195     1.431

   2                toyindiv:2     M     0.221     0.027      0.218     0.054        5.712     0.532      5.901     1.877

   3                toyindiv:3     F     0.183     0.032      0.201     0.053        3.656     0.539      5.388     1.554

   4                toyindiv:4     M     0.289     0.033      0.258     0.056        5.018     0.760      4.308     1.549

 

 

###ALLELE FREQUENCY ESTIMATES WITH STANDARD ERROR

##SNP_Index: marker internal index num

##amean and bmean are the average reference allele frequency for population A and B

##asdev and bsdev are the corresponding standard deviation

 

SNP_Index Chr_Num          SNP_ID   amean   asdev     bmean     bsdev

    0   1             rs819980     0.948     0.006        0.030     0.016

    1   1           rs10907185     0.252     0.010        0.680     0.024

    4   1             rs897634     0.090     0.006        0.782     0.020

    6   1            rs2817159     0.950     0.006        0.074     0.015

    9   1            rs1181868     0.910     0.008        0.241     0.022

   12   1            rs7548756     0.830     0.009        0.209     0.022

   16   1            rs2012852     0.823     0.010        0.297     0.023

 

 

###LAG AND CORRELATIONS

 

               llike mean: -37738.643 s.err:  1552.579

lag:  1 corr:     0.356 sig:     3.544

lag:  2 corr:     0.221 sig:     2.188

lag:  3 corr:     0.264 sig:     2.599

 

 

lag:  9 corr:    -0.071 sig:    -0.674

lag: 10 corr:    -0.131 sig:    -1.241

  • Scores for each marker
  • Scores for each chromosome, and as one can clearly see from the below example, the LGS_MAX and CCS_MAX scores are the highest for chromosome number 3.
  • Bestscores: The maximum genome-wide score for the locus-genome statistic, and the maximum and minimum genome-wide scores for the case-control statistic.
  • Genome-log-factor: log-likelihood of the locus genome statistic averaged over all the markers in the genome. The genome-log-factor is the most important number that is produced by the program and should be the first number that the user looks at.

###SCORES FOR EACH MARKER (fakes used for global score)

##LGS: locus genome statistic score, CCS:case control statistic

###SNP_Index    Chr               SNP_ID    Phys_Pos    Gen_Pos       LGS        CCS         G(case) G(control)     rpower

           0      1             rs819980   1510967        0.032    -3.574      0.647         0.208      0.197      0.800

           1      1           rs10907185   1765381        0.035    -3.620      0.615         0.208      0.197      0.787

           2      1             fake-1:0   2002021        0.040    -3.593      0.667         0.208      0.197      0.772

           3      1             fake-1:1   2516231        0.050    -3.686      0.769         0.208      0.195      0.774

           4      1             rs897634   2858849        0.057    -3.862      0.824         0.208      0.194      0.806

           5      1             fake-1:2   2959423        0.060    -3.729      0.966         0.208      0.192      0.805

           6      1            rs2817159   3172565        0.067    -3.562      1.253         0.209      0.189      0.831

 

 

        5422     23            rs7054554 150935421        1.185    -3.943      0.232         0.186      0.186      0.720

        5423     23         fake-23:3620 151499820        1.190    -3.918      0.204         0.185      0.187      0.701

        5424     23         fake-23:3621 152532006        1.200    -3.919      0.152         0.185      0.187      0.683

        5425     23           rs10127175 152805019        1.203    -3.929      0.138         0.185      0.187      0.681

        5426     23             rs884840 153491735        1.206    -3.943      0.119         0.184      0.188      0.680

 

###SCORES FOR EACH CHROMOSOME

##LGS_MAX: Maximum locus genome statistic score

##CCS_MAX and CCS_MIN are the maximum and minimum case control statistic scores

##LGS_LOCAL: log likelihood of the locus genome statistic score obtained by averaging over all the markers on that chromosome

   Chr_Num  LGS_MAX   CCS_MAX  CCS_MIN  LGS_LOCAL

 

    1  -0.35    1.79  -2.23   -2.06

    2  16.60    7.31  -1.04   14.77

    3  -2.94    1.69  -0.80   -4.21

    4  -2.59    1.77  -1.83   -4.02

    5  -3.22    1.28  -2.11   -4.56

    6  -2.72    0.59  -2.23   -4.03

    7  -0.97    2.29  -0.79   -2.29

    8  -3.62    0.30  -2.46   -4.76

    9  -1.64    1.17  -1.11   -3.05

   10  -3.15    1.31  -1.93   -4.45

   11  -1.99    2.34  -1.22   -3.18

   12   1.32    2.25  -2.16   -0.09

   13  -1.29    2.40  -1.27   -2.33

   14  -1.08    1.42  -1.41   -2.30

   15  -2.61    0.36  -2.07   -3.99

   16  -2.72    0.27  -2.34   -3.77

   17  -0.10    0.96  -0.96   -1.52

   18  -1.12    2.24  -2.90   -2.32

   19  -0.81    2.38  -0.98   -2.50

   20  -0.20    1.01  -0.42   -1.92

   21  -1.36    3.01  -0.19   -2.95

   22  -3.39    2.14  -1.13   -4.36

   23  -1.51    2.44  -1.67   -2.50

 

###BESTSCORES: Maximum genome-wide score for the locus-genome statistic (LGS_MAX), and the maximum and minimum genome-wide scores fo

r the case-control statistic (CCS_MAX and CCS_MIN)

bestscores:     16.600     7.310    -2.900

 

###GENOME LOG FACTOR: log-likelihood of the locus genome statistic averaged over all the markers in the genome

genome log-factor:    13.633

##end of run