[Haplostats] EM is not ignoring missing data #41
Description
Using the same .ini and .pop files as in Issue #40 , it looks like [Haplostats] is including missing data (****) in its haploype estimation.
Here is an example of [Emhaplofreq] results:
Haplotype frequency est. for loci: A:B:DRB1
-------------------------------------------
Number of individuals: 47 (before-filtering)
Number of individuals: 45 (after-filtering)
Unique phenotypes: 45
Unique genotypes: 113
Number of haplotypes: 188
Loglikelihood under linkage equilibrium [ln(L_0)]: -359.216808
Loglikelihood obtained via the EM algorithm [ln(L_1)]: -340.336732
Number of iterations before convergence: 44
Haplotypes sorted by name | Haplotypes sorted by frequency
haplotype frequency# copies| haplotype frequency# copies
0101~1301~0402 0.02222 2.0 | 0201~1401~0402 0.04444 4.0
0101~1301~1101 0.01111 1.0 | 03012~1401~0407 0.03333 3.0
0101~1401~0901 0.01111 1.0 | 03012~1301~0402 0.03333 3.0
0101~1520~1602 0.01111 1.0 | 0201~1401~0802 0.03333 3.0
0101~18012~0407 0.01111 1.0 | 3204~1401~0802 0.02222 2.0
0101~39021~0404 0.01111 1.0 | 0201~1401~1101 0.02222 2.0
0101~39021~1602 0.01111 1.0 | 0101~4005~0802 0.02222 2.0
0101~4005~0802 0.02222 2.0 | 03012~39021~0402 0.02222 2.0
0101~67011~0802 0.01111 1.0 | 0201~1301~1602 0.02222 2.0
0101~8101~1602 0.01111 1.0 | 0218~1401~0404 0.02222 2.0
0201~1301~1602 0.02222 2.0 | 0210~51013~1602 0.02222 2.0
0201~1401~0402 0.04444 4.0 | 0218~1401~0802 0.02222 2.0
0201~1401~0404 0.01111 1.0 | 0101~1301~0402 0.02222 2.0
0201~1401~0407 0.01111 1.0 | 2501~4005~0802 0.02222 2.0
0201~1401~0802 0.03333 3.0 | 2501~1301~0802 0.02222 2.0
0201~1401~0901 0.01111 1.0 | 2501~39021~0402 0.02222 2.0
0201~1401~1101 0.02222 2.0 | 3204~39021~0802 0.02222 2.0
0201~18012~0407 0.01111 1.0 | 03012~1520~0802 0.02222 2.0
0201~39021~0901 0.01111 1.0 | 0201~1401~0901 0.01111 1.0
0201~4005~0402 0.01111 1.0 | 0101~39021~1602 0.01111 1.0
0201~51013~0802 0.01111 1.0 | 0210~1301~0407 0.01111 1.0
0201~5703~1101 0.01111 1.0 | 0218~35091~0901 0.01111 1.0
0210~1301~0402 0.01111 1.0 | 0210~78021~0901 0.01111 1.0
0210~1301~0407 0.01111 1.0 | 3204~1301~0901 0.01111 1.0
0210~1401~0404 0.01111 1.0 | 3204~51013~1101 0.01111 1.0
0210~35091~0402 0.01111 1.0 | 2501~1401~0404 0.01111 1.0
0210~39021~0802 0.01111 1.0 | 6814~1520~0407 0.01111 1.0
0210~4005~0802 0.01111 1.0 | 0201~18012~0407 0.01111 1.0
0210~51013~1602 0.02222 2.0 | 0201~4005~0402 0.01111 1.0
0210~78021~0901 0.01111 1.0 | 0101~8101~1602 0.01111 1.0
0218~1301~0402 0.01111 1.0 | 0210~1301~0402 0.01111 1.0
0218~1401~0402 0.01111 1.0 | 6901~1301~0402 0.01111 1.0
0218~1401~0404 0.02222 2.0 | 0210~4005~0802 0.01111 1.0
0218~1401~0407 0.01111 1.0 | 03012~4005~0802 0.01111 1.0
0218~1401~0802 0.02222 2.0 | 0101~1401~0901 0.01111 1.0
0218~35091~0901 0.01111 1.0 | 0101~1301~1101 0.01111 1.0
0218~4005~1101 0.01111 1.0 | 0101~1520~1602 0.01111 1.0
03012~1301~0402 0.03333 3.0 | 0218~1301~0402 0.01111 1.0
03012~1401~0407 0.03333 3.0 | 0201~51013~0802 0.01111 1.0
03012~1401~0802 0.01111 1.0 | 0201~39021~0901 0.01111 1.0
03012~1520~0802 0.02222 2.0 | 2501~1520~0404 0.01111 1.0
03012~39021~0402 0.02222 2.0 | 6814~5703~1602 0.01111 1.0
03012~39021~0802 0.01111 1.0 | 0201~1401~0404 0.01111 1.0
03012~4005~0802 0.01111 1.0 | 0201~1401~0407 0.01111 1.0
03012~51013~0901 0.01111 1.0 | 3204~1301~1602 0.01111 1.0
2501~1301~0802 0.02222 2.0 | 0218~1401~0407 0.01111 1.0
2501~1401~0404 0.01111 1.0 | 0218~4005~1101 0.01111 1.0
2501~1520~0404 0.01111 1.0 | 03012~1401~0802 0.01111 1.0
2501~39021~0402 0.02222 2.0 | 03012~39021~0802 0.01111 1.0
2501~4005~0802 0.02222 2.0 | 0101~39021~0404 0.01111 1.0
2501~51013~0901 0.01111 1.0 | 0210~1401~0404 0.01111 1.0
2501~5703~0802 0.01111 1.0 | 6814~4005~0407 0.01111 1.0
2501~8101~0802 0.01111 1.0 | 0101~18012~0407 0.01111 1.0
3204~1301~0901 0.01111 1.0 | 6901~1520~0402 0.01111 1.0
3204~1301~1602 0.01111 1.0 | 0210~35091~0402 0.01111 1.0
3204~1401~0802 0.02222 2.0 | 0210~39021~0802 0.01111 1.0
3204~1520~0802 0.01111 1.0 | 03012~51013~0901 0.01111 1.0
3204~39021~0802 0.02222 2.0 | 6901~67011~1602 0.01111 1.0
3204~51013~1101 0.01111 1.0 | 0218~1401~0402 0.01111 1.0
6814~1520~0407 0.01111 1.0 | 0101~67011~0802 0.01111 1.0
6814~4005~0407 0.01111 1.0 | 2501~8101~0802 0.01111 1.0
6814~5703~1602 0.01111 1.0 | 7403~39021~0407 0.01111 1.0
6901~1301~0402 0.01111 1.0 | 6901~1301~0404 0.01111 1.0
6901~1301~0404 0.01111 1.0 | 2501~5703~0802 0.01111 1.0
6901~1520~0402 0.01111 1.0 | 2501~51013~0901 0.01111 1.0
6901~67011~1602 0.01111 1.0 | 0201~5703~1101 0.01111 1.0
7403~39021~0407 0.01111 1.0 | 3204~1520~0802 0.01111 1.0
And here is an example of [Haplostats] results:
II. Multi-locus Analyses [haplo-stats]
======================================
Haplotype / linkage disequilibrium (LD) statistics
__________________________________________________
Pairwise LD estimates
---------------------
Locus pair D D' Wn ln(L_1) ln(L_0) S # permu p-value
A:B *0.516108 0.390722 -314.17 NaN - -
Haplotype frequency est. for loci: A:B
--------------------------------------
Unique genotypes: 50
Number of haplotypes: 52
Loglikelihood under linkage equilibrium [ln(L_0)]:
Loglikelihood obtained via the EM algorithm [ln(L_1)]: -314.173
Number of iterations before convergence:
Haplotypes sorted by name | Haplotypes sorted by frequency
haplotype frequency# copies| haplotype frequency# copies
****~1301 0.0106382 | 0201~1401 0.1271851
****~1401 0.0106382 | 0218~1401 0.0638297
****~18012 0.0106382 | 03012~1401 0.0319148
****~78021 0.0106382 | 0101~1301 0.0319148
0101~1301 0.0319148 | 0210~1301 0.0319148
0101~1401 0.0111127 | 2501~1301 0.0319148
0101~1520 0.0212765 | 03012~1520 0.0319148
0101~35091 0.0106382 | 03012~51013 0.0319148
0101~39021 0.0208021 | 2501~39021 0.0319146
0101~51013 0.0106382 | 3204~39021 0.0212768
0101~8101 0.0212765 | 0101~1520 0.0212765
0201~1301 0.0212765 | 0101~8101 0.0212765
0201~1401 0.1271851 | 0201~1301 0.0212765
0201~18012 0.0106382 | 0201~4005 0.0212765
0201~39021 0.0111127 | 0210~4005 0.0212765
0201~4005 0.0212765 | 0218~4005 0.0212765
0201~5703 0.0106382 | 2501~51013 0.0212765
0210~1301 0.0319148 | 03012~1301 0.0212765
0210~1401 0.0212765 | 03012~39021 0.0212765
0210~35091 0.0106382 | 3204~1401 0.0212765
0210~39021 0.0106382 | 6901~1301 0.0212765
0210~4005 0.0212765 | 0210~1401 0.0212765
0210~51013 8.1821857 | 0101~39021 0.0208021
0218~1301 0.0106382 | 0101~1401 0.0111127
0218~1401 0.0638297 | 0201~39021 0.0111127
0218~4005 0.0212765 | 0101~35091 0.0106382
03012~1301 0.0212765 | 0101~51013 0.0106382
03012~1401 0.0319148 | 0201~5703 0.0106382
03012~1520 0.0319148 | 0201~18012 0.0106382
03012~39021 0.0212765 | 0210~35091 0.0106382
03012~4005 0.0106382 | 0210~39021 0.0106382
03012~51013 0.0319148 | 0218~1301 0.0106382
2501~1301 0.0319148 | 2501~1401 0.0106382
2501~1401 0.0106382 | 2501~5703 0.0106382
2501~39021 0.0319146 | 2501~67011 0.0106382
2501~4005 2.9233526 | 03012~4005 0.0106382
2501~51013 0.0212765 | 3204~1301 0.0106382
2501~5703 0.0106382 | 3204~1520 0.0106382
2501~67011 0.0106382 | 3204~78021 0.0106382
3204~1301 0.0106382 | 6814~1520 0.0106382
3204~1401 0.0212765 | 6814~4005 0.0106382
3204~1520 0.0106382 | 6814~5703 0.0106382
3204~39021 0.0212768 | 6901~18012 0.0106382
3204~4005 0.0106380 | 6901~67011 0.0106382
3204~78021 0.0106382 | 7403~39021 0.0106382
6814~1520 0.0106382 | ****~1301 0.0106382
6814~4005 0.0106382 | ****~1401 0.0106382
6814~5703 0.0106382 | ****~18012 0.0106382
6901~1301 0.0212765 | ****~78021 0.0106382
6901~18012 0.0106382 | 3204~4005 0.0106380
6901~67011 0.0106382 | 2501~4005 2.9233526
7403~39021 0.0106382 | 0210~51013 8.1821857