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