TDT2G: A 2-groups Χ2 multimarker TDT for genome-wide exploration
Supplementary material
Simulations
Download a detailed description of the way simulations were performed
Download a detailed description of the configurations used to run msHOT
trioSampling: software used to generate trio SNP genotype samples from populations
Power and locus specificity: Comparisons among several multimarker TDTs using samples with 200 trios
One locus
Figure S1. Simulations for haplotype width 2
Figure S2. Simulations for haplotype width 4
Figure S3. Simulations for haplotype width 6
Figure S4. Simulations for haplotype width 8
Figure S5. Simulations for haplotype width 10
Two loci: Additive - DomOrDom - RecOrRec disease models
Figure S6. Simulations for haplotype width 2
Figure S7. Simulations for haplotype width 4
Figure S8. Simulations for haplotype width 6
Figure S9. Simulations for haplotype width 8
Figure S10. Simulations for haplotype width 10
Two loci: DomAndDom - Threshold - Modified disease models
Figure S11. Simulations for haplotype width 2
Figure S12. Simulations for haplotype width 4
Figure S13. Simulations for haplotype width 6
Figure S14. Simulations for haplotype width 8
Figure S15. Simulations for haplotype width 10
Power and locus specificity using samples with 500 trios and low relative risks: TDT2G, TDT2G-cv5 and TDTS
One locus
Figure S16. Simulations for haplotype width 1
Figure S17. Simulations for haplotype width 2
Figure S18. Simulations for haplotype width 4
Figure S19. Simulations for haplotype width 6
Figure S20. Simulations for haplotype width 8
Figure S21. Simulations for haplotype width 10
Two loci: Additive - DomOrDom - RecOrRec disease models
Figure S22. Simulations for haplotype width 1
Figure S23. Simulations for haplotype width 2
Figure S24. Simulations for haplotype width 4
Figure S25. Simulations for haplotype width 6
Figure S26. Simulations for haplotype width 8
Figure S27. Simulations for haplotype width 10
Two loci: DomAndDom - Threshold - Modified disease models
Figure S28. Simulations for haplotype width 1
Figure S29. Simulations for haplotype width 2
Figure S30. Simulations for haplotype width 4
Figure S31. Simulations for haplotype width 6
Figure S32. Simulations for haplotype width 8
Figure S33. Simulations for haplotype width 10
Test reproducibility: TDT2G and TDTS
One locus
Figure S34. Simulations for haplotype width 1
Figure S35. Simulations for haplotype width 2
Figure S36. Simulations for haplotype width 4
Figure S37. Simulations for haplotype width 6
Figure S38. Simulations for haplotype width 8
Figure S39. Simulations for haplotype width 10
Two loci: Additive - DomOrDom - RecOrRec disease models
Figure S40. Simulations for haplotype width 1
Figure S41. Simulations for haplotype width 2
Figure S42. Simulations for haplotype width 4
Figure S43. Simulations for haplotype width 6
Figure S44. Simulations for haplotype width 8
Figure S45. Simulations for haplotype width 10
Two loci: DomAndDom - Threshold - Modified disease models
Figure S46. Simulations for haplotype width 1
Figure S47. Simulations for haplotype width 2
Figure S48. Simulations for haplotype width 4
Figure S49. Simulations for haplotype width 6
Figure S50. Simulations for haplotype width 8
Figure S51. Simulations for haplotype width 10
Real data
Sliding window maps
Figure S52 Sliding window maps for window width of 1
Figure S53 Sliding window maps for window width of 2
Figure S54 Sliding window maps for window width of 4
Figure S55 Sliding window maps for window width of 6
Figure S56 Sliding window maps for window width of 8
Figure S57 Sliding window maps for window width of 10
CTDT maps
Figure S58 CTDT maps for window width of 1
Figure S59 CTDT maps for window width of 2
Figure S60 CTDT maps for window width of 4
Figure S61 CTDT maps for window width of 6
Figure S62 CTDT maps for window width of 8
Figure S63 CTDT maps for window width of 10
Data sets
Crohn data set in makeped format
CEU IHMP data set in makeped format same locus as Crohn data set
Software
Download source code
Download compiled version for linux 64
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