Skip to content

Commit

Permalink
output the haplotypes (using lociToEstHaplo=* in .ini file)
Browse files Browse the repository at this point in the history 
convert test to compare file output
  • Loading branch information
@alexlancaster
alexlancaster committed Aug 5, 2017
1 parent 7f678de commit e24add2
Show file tree
Hide file tree
Showing 4 changed files with 2,178 additions and 2 deletions.
1 change: 1 addition & 0 deletions tests/data/minimal.ini
View file
Original file line number Diff line number Diff line change
Expand Up @@ -65,6 +65,7 @@ numReplicates=10000
;; and 'dqb1' loci. A wildcard entry '*' means estimate haplotypes
;; for the entire loci as specified in the original file column order
;;lociToEstHaplo=a:b:drb1,a:b:c,drb1:dqa1:dpb1,drb1:dqb1:dpb1
lociToEstHaplo=*

;; analogous to `lociToEst' except for linkage disequilibrium (LD)
;;lociToEstLD=
Expand Down
253 changes: 253 additions & 0 deletions tests/data/output/USAFEL-UchiTelle-small-out.txt
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,253 @@
Results of data analysis
Performed on the 'USAFEL-UchiTelle-small.pop' file at:


Population Summary
==================
Population Name: UchiTelle
Lab code: USAFEL
Typing method: 12th Workshop SSOP
Ethnicity: Telle
Continent: NW Asia
Collection site: Targen Village
Latitude: 41 deg 12 min N
Longitude: 94 deg 7 min E
complex: 1


Population Totals
_________________
Sample Size (n): 10
Allele Count (2n): 20
Total loci in file: 3 [A, C, B]
Total loci with data: 3 [A, C, B]


Legend for all analyses
_______________________

* = significant at the 5% level
** = significant at the 1% level
*** = significant at the 0.1% level
**** = significant at the 0.01% level
***** = significant at the 0.001% level


I. Single Locus Analyses
========================

1. Locus: A
___________

1.1. Allele Counts [A]
----------------------
Untyped individuals: 2.0
Sample Size (n): 8.0
Allele Count (2n): 16
Distinct alleles (k): 8

Counts ordered by freque| Counts ordered by name
Name Frequency (Count) | Name Frequency (Count)
0201 0.25000 4 | 0101 0.06250 1
3204 0.18750 3 | 0201 0.25000 4
0210 0.12500 2 | 0210 0.12500 2
03012 0.12500 2 | 0218 0.06250 1
2501 0.12500 2 | 03012 0.12500 2
0101 0.06250 1 | 2501 0.12500 2
0218 0.06250 1 | 3204 0.18750 3
6814 0.06250 1 | 6814 0.06250 1
Total 1.00000 16 | Total 1.00000 16


1.2. HardyWeinberg [A]
----------------------
Table of genotypes, format of each cell is: observed/expected.

0101 0/0.0
0201 0/0.3 1/0.5
0210 0/0.1 0/0.5 0/0.1
0218 1/0.1 0/0.3 0/0.1 0/0.0
03012 0/0.1 0/0.5 1/0.3 0/0.1 0/0.1
2501 0/0.1 1/0.5 0/0.3 0/0.1 0/0.3 0/0.1
3204 0/0.2 0/0.8 1/0.4 0/0.2 1/0.4 1/0.4 0/0.3
6814 0/0.1 1/0.3 0/0.1 0/0.1 0/0.1 0/0.1 0/0.2 0/0.0
0101 0201 0210 0218 03012 2501 3204 6814
[Cols: 1 to 8]

Observed Expected Chi-square DoF p-value
------------------------------------------------------------------------------------------
Common No commmon genotypes; chi-square cannot be calculated

------------------------------------------------------------------------------------------
Lumped genotypes Value not calculated.

------------------------------------------------------------------------------------------
Common + lumped Value not calculated.

------------------------------------------------------------------------------------------
All heterozygotes 7 6.75 0.01 1 0.9233
------------------------------------------------------------------------------------------
Common heterozygotes by allele

------------------------------------------------------------------------------------------
Common genotypes
Total 0 0.00
------------------------------------------------------------------------------------------


1.3. Guo and Thompson HardyWeinberg output (monte-carlo) [A]
------------------------------------------------------------
Steps in Monte-Carlo randomization: 100000
p-value (overall): 0.8115

Individual genotype p-values found to be significant
Genotype (observed/expected) [Chen's pval] [diff pval]


1.4. Slatkin's implementation of EW homozygosity test of neutrality [A]
-----------------------------------------------------------------------
Observed F: 0.1562, Expected F: 0.1886, Variance in F: 0.0013
Normalized deviate of F (Fnd): -0.9076, p-value of F: 0.2121


2. Locus: C
___________

2.1. Allele Counts [C]
----------------------
Untyped individuals: 0.0
Sample Size (n): 10.0
Allele Count (2n): 20
Distinct alleles (k): 9

Counts ordered by freque| Counts ordered by name
Name Frequency (Count) | Name Frequency (Count)
0102 0.20000 4 | 0102 0.20000 4
0307 0.20000 4 | 02025 0.10000 2
02025 0.10000 2 | 0307 0.20000 4
0605 0.10000 2 | 0605 0.10000 2
0712 0.10000 2 | 0712 0.10000 2
1202 0.10000 2 | 0804 0.05000 1
1507 0.10000 2 | 1202 0.10000 2
0804 0.05000 1 | 1507 0.10000 2
1801 0.05000 1 | 1801 0.05000 1
Total 1.00000 20 | Total 1.00000 20


2.2. HardyWeinberg [C]
----------------------
Table of genotypes, format of each cell is: observed/expected.

0102 0/0.4
02025 1/0.4 0/0.1
0307 0/0.8 0/0.4 1/0.4
0605 0/0.4 0/0.2 1/0.4 0/0.1
0712 2/0.4 0/0.2 0/0.4 0/0.2 0/0.1
0804 0/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/0.0
1202 0/0.4 1/0.2 0/0.4 0/0.2 0/0.2 1/0.1 0/0.1
1507 0/0.4 0/0.2 1/0.4 1/0.2 0/0.2 0/0.1 0/0.2 0/0.1
1801 1/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/0.1 0/0.1 0/0.1 0/0.0
0102 02025 0307 0605 0712 0804 1202 1507 1801
[Cols: 1 to 9]

Observed Expected Chi-square DoF p-value
------------------------------------------------------------------------------------------
Common No commmon genotypes; chi-square cannot be calculated

------------------------------------------------------------------------------------------
Lumped genotypes Value not calculated.

------------------------------------------------------------------------------------------
Common + lumped Value not calculated.

------------------------------------------------------------------------------------------
All heterozygotes 9 8.65 0.01 1 0.9053
------------------------------------------------------------------------------------------
Common heterozygotes by allele

------------------------------------------------------------------------------------------
Common genotypes
Total 0 0.00
------------------------------------------------------------------------------------------


2.3. Guo and Thompson HardyWeinberg output (monte-carlo) [C]
------------------------------------------------------------
Steps in Monte-Carlo randomization: 100000
p-value (overall): 0.4779

Individual genotype p-values found to be significant
Genotype (observed/expected) [Chen's pval] [diff pval]
0712+0102 (2/0.400000) 0.0347* 0.0376*


2.4. Slatkin's implementation of EW homozygosity test of neutrality [C]
-----------------------------------------------------------------------
Observed F: 0.1350, Expected F: 0.1789, Variance in F: 0.0014
Normalized deviate of F (Fnd): -1.1641, p-value of F: 0.0668


3. Locus: B
___________

3.1. Allele Counts [B]
----------------------
Untyped individuals: 1.0
Sample Size (n): 9.0
Allele Count (2n): 18
Distinct alleles (k): 1

Counts ordered by frequ| Counts ordered by name
Name Frequency (Count) | Name Frequency (Count)
1301 1.00000 18 | 1301 1.00000 18
Total1.00000 18 | Total1.00000 18

[Locus is monomorphic, so no further analyses performed]




II. Multi-locus Analyses
========================

Haplotype / linkage disequilibrium (LD) statistics
__________________________________________________

Pairwise LD estimates
---------------------
Locus pair D D' Wn ln(L_1) ln(L_0) S # permu p-value
A:C 0.04309 1.20192 2.43975 -36.04 -50.35 28.61 - -
A:B nan inf inf -26.51 -28.42 3.82 - -
C:B nan inf inf -32.10 -21.53 -21.13 - -


Haplotype frequency est. for loci: A:C:B
----------------------------------------
Number of individuals: 10 (before-filtering)
Number of individuals: 8 (after-filtering)
Unique phenotypes: 8
Unique genotypes: 14
Number of haplotypes: 26
Loglikelihood under linkage equilibrium [ln(L_0)]: -50.350627
Loglikelihood obtained via the EM algorithm [ln(L_1)]: -36.043653
Number of iterations before convergence: 22

Haplotypes sorted by name | Haplotypes sorted by frequency
haplotype frequency# copies| haplotype frequency# copies
0101~0804~1301 0.06250 1.0 | 0210~0102~1301 0.12500 2.0
0201~0102~1301 0.06250 1.0 | 2501~0307~1301 0.12500 2.0
0201~02025~1301 0.06250 1.0 | 03012~0712~1301 0.06250 1.0
0201~1202~1301 0.06250 1.0 | 0101~0804~1301 0.06250 1.0
0201~1507~1301 0.06250 1.0 | 0218~1202~1301 0.06250 1.0
0210~0102~1301 0.12500 2.0 | 0201~1507~1301 0.06250 1.0
0218~1202~1301 0.06250 1.0 | 3204~1801~1301 0.06250 1.0
03012~0605~1301 0.06250 1.0 | 03012~0605~1301 0.06250 1.0
03012~0712~1301 0.06250 1.0 | 3204~1507~1301 0.06250 1.0
2501~0307~1301 0.12500 2.0 | 3204~0307~1301 0.06250 1.0
3204~0307~1301 0.06250 1.0 | 0201~0102~1301 0.06250 1.0
3204~1507~1301 0.06250 1.0 | 6814~0712~1301 0.06250 1.0
3204~1801~1301 0.06250 1.0 | 0201~02025~1301 0.06250 1.0
6814~0712~1301 0.06250 1.0 | 0201~1202~1301 0.06250 1.0



Loading

0 comments on commit e24add2

Please sign in to comment.