| Limitation of data |
V3
| V4
| V5
| V6
| V7
| V8
| V9
| Remarks
|
| samples |
Standard |
1,000 |
|
| Pro |
10,000 |
|
| Genotyping Data Import |
V3
| V4
| V5
| V6
| V7
| V8
| V9
| Remarks
|
| Excel file |
 |
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 |
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Support Excel 2007(xlsx format) |
Tab Separated Values File
Text File |
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Biotage company
PSQ96 export file |
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ABI company PRISM7900
export file |
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| Multiple open of data-sheet |
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Support to open multiple data-sheets |
SNPAlyze Data file
(Treat genotyping data and all analysis data collectively) |
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| Case-Control Study |
V3
| V4
| V5
| V6
| V7
| V8
| V9
| Remarks
|
| loci |
2,560 |
|
| group |
10 |
|
| Settings of a counting method for DNA polymorphism |
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Define the size of contingency table |
| Chi-square test |
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Calculate Chi-square and p-value |
| Utilization of AIC |
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| Fisher’s exact test (2 x 2) |
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Only the case of a 2X2 contingency table |
| Fisher’s exact test (m x n) |
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Corresponds to mXn contingency table |
| Calculation of Odds ratio |
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Only the case of a 2X2 contingency table |
| Cluster Analysis |
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Output Dendrogram and Dissimilarity matrix |
| Save an analysis result as Excel format |
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Support Excel 2007(xlsx format) |
| Utilization of Bootstrap method |
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Output Chi-square, p-value, AIC, Mean of Odds ratio, Dispersion and Standard deviation |
| Output Details Information |
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| Corresponds to microsatellite data |
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| Automatically define contingency tables |
|
 |
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Except for the recessive and dominant model |
| Multiple testing correction |
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BH or Bootstrap method is available |
| Linkage Disequilibrium Analysis |
V3
| V4
| V5
| V6
| V7
| V8
| V9
| Remarks
|
| loci |
1,000 |
|
| group |
5 |
|
| Output Haplotype frequency |
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Utilization of EM algorithm |
| Linkage Disequilibrium coefficient |
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Calculate D, D’, D’,(abs) and r2 |
| Chi-square test |
|
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Calculate Chi-square and p-value
|
| Utilization of AIC |
|
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| Graphical display of Linkage Disequilibrium (Grid format) |
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| Graphical display of Linkage Disequilibrium (BMP format) |
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| Save an analysis result as Excel format |
|
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Graphical display of Linkage Disequilibrium (Grid format only)
Support Excel 2007(xlsx format) |
| Utilization of Bootstrap method |
|
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Output LD coefficient, Chi-square, p-value, Mean of AIC, Dispersion and Standard deviation |
| Corresponds to microsatellite data |
|
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| Haplotype Inference |
V3
| V4
| V5
| V6
| V7
| V8
| V9
| Remarks
|
| loci |
Standard |
30 |
|
| Pro |
40 |
|
| group |
5 |
|
| Estimate Haplotype frequency |
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Utilization of EM algorithm |
| Estimate Haplotype frequency in consideration of the missing data |
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| Estimate Diplotypes of each sample |
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| Estimate Diplotype distribution |
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| Save an analysis result as Excel format |
|
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|
|
Support Excel 2007 (xlsx format) |
| Utilization of Bootstrap method |
|
|
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|
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|
|
Output Mean of Haplotype frequency, Dispersion and Standard deviation |
| Corresponds to microsatellite data |
|
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| htSNP identification |
|
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Output only one set of htSNPs |
| Save each diplotype combination as text |
|
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| Hardy-Weinberg Equilibrium Test |
V3
| V4
| V5
| V6
| V7
| V8
| V9
| Remarks
|
| loci |
2,560 |
|
| group |
5 |
|
| Chi-square test |
|
|
|
|
|
|
|
Calculate Chi-square and p-value |
| Output Details Information |
|
|
|
|
|
|
|
|
| Corresponds to microsatellite data |
|
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| Exact test |
|
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Evaluation of exact test and Exact test (Monte carlo simulation) |
| Save an analysis result as Excel format |
|
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| Multiple testing correction |
|
|
|
|
|
|
|
BH or Bootstrap method is available |
| Cochran-Armitage Trend Test |
V3
| V4
| V5
| V6
| V7
| V8
| V9
| Remarks
|
| loci |
|
|
|
|
|
2,560 |
|
| group |
|
|
|
|
|
2 |
|
| Chi-square test |
|
|
|
|
|
|
|
Calculate Chi-square and p-value |
| Output Details Information |
|
|
|
|
|
|
|
|
| Corresponds to microsatellite data |
|
|
|
|
|
|
|
|
| Save an analysis result as Excel format |
|
|
|
|
|
|
|
|
| Multiple testing correction |
|
|
|
|
|
|
|
BH or Bootstrap method is available |
| Case-Control Haplotype Analysis |
V3
| V4
| V5
| V6
| V7
| V8
| V9
| Remarks
|
| loci |
10 |
|
| group |
5 |
|
| Testing Haplotype frequency between Populations |
|
|
|
|
|
|
|
Utilization of Permutation test and Chi-square test |
| Testing the difference of each Haplotype frequency between groups |
|
|
|
|
|
|
|
Utilization of Permutation test and Chi-square test |
| Output a graph of Frequency distribution |
|
|
|
|
|
|
|
|
| Corresponds to microsatellite data |
|
|
|
|
|
|
|
|
| Calculation of Odds ratio |
|
|
|
|
|
|
|
Only the case of a 2×2 contingency table |
| Haplotype Block Analysis |
V3
| V4
| V5
| V6
| V7
| V8
| V9
| Remarks
|
| loci |
1,000 |
|
| Gabriel method |
|
|
|
|
|
|
|
|
| Four Gamete method |
|
|
|
|
|
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|
|
| htSNP identification |
|
|
|
|
|
|
|
|
| Graphical display of Haplotype Block |
|
|
|
|
|
|
|
|
| Manual selection of Haplotype Block |
|
|
|
|
|
|
|
|
| LD co-efficient between two blocks |
|
|
|
|
|
|
|
Display the D’-value between two blocks |
| Chi-square test |
|
|
|
|
|
|
|
|
| Cooperate with HealthSketch |
V3
| V4
| V5
| V6
| V7
| V8
| V9
| Remarks
|
| Data passing between SNPAlyze and HealthSketch |
|
|
|
|
|
|
|
HealthSketch Ver.1.1 or later is required |
| Logistic Regression Analysis |
|
|
|
|
|
|
|
HealthSketch Ver.2.5 or later is required |
