TDTP: A highly locus-specific 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

One locus

Figure S1. Simulations for haplotype width 1
Figure S2. Simulations for haplotype width 2
Figure S3. Simulations for haplotype width 4
Figure S4. Simulations for haplotype width 6
Figure S5. Simulations for haplotype width 8
Figure S6. Simulations for haplotype width 10

Two loci: Additive - DomOrDom - RecOrRec disease models

Figure S7. Simulations for haplotype width 1
Figure S8. Simulations for haplotype width 2
Figure S9. Simulations for haplotype width 4
Figure S10. Simulations for haplotype width 6
Figure S11. Simulations for haplotype width 8
Figure S12. Simulations for haplotype width 10

Two loci: DomAndDom - Threshold - Modified disease models

Figure S13. Simulations for haplotype width 1
Figure S14. Simulations for haplotype width 2
Figure S15. Simulations for haplotype width 4
Figure S16. Simulations for haplotype width 6
Figure S17. Simulations for haplotype width 8
Figure S18. Simulations for haplotype width 10

Comparisons with test for the small data problem

One locus

Figure S19. Simulations for haplotype width 1
Figure S20. Simulations for haplotype width 2
Figure S21. Simulations for haplotype width 4
Figure S22. Simulations for haplotype width 6
Figure S23. Simulations for haplotype width 8
Figure S24. Simulations for haplotype width 10

Two loci: Additive - DomOrDom - RecOrRec disease models

Figure S25. Simulations for haplotype width 1
Figure S26. Simulations for haplotype width 2
Figure S27. Simulations for haplotype width 4
Figure S28. Simulations for haplotype width 6
Figure S29. Simulations for haplotype width 8
Figure S30. Simulations for haplotype width 10

Two loci: DomAndDom - Threshold - Modified disease models

Figure S31. Simulations for haplotype width 1
Figure S32. Simulations for haplotype width 2
Figure S33. Simulations for haplotype width 4
Figure S34. Simulations for haplotype width 6
Figure S35. Simulations for haplotype width 8
Figure S36. Simulations for haplotype width 10

Results using samples of 500 trios and low relative risks

One locus

Figure S37. Simulations for haplotype width 1
Figure S38. Simulations for haplotype width 2
Figure S39. Simulations for haplotype width 4
Figure S40. Simulations for haplotype width 6
Figure S41. Simulations for haplotype width 8
Figure S42. Simulations for haplotype width 10

Two loci: Additive - DomOrDom - RecOrRec disease models

Figure S43. Simulations for haplotype width 1
Figure S44. Simulations for haplotype width 2
Figure S45. Simulations for haplotype width 4
Figure S46. Simulations for haplotype width 6
Figure S47. Simulations for haplotype width 8
Figure S48. Simulations for haplotype width 10

Two loci: DomAndDom - Threshold - Modified disease models

Figure S49. Simulations for haplotype width 1
Figure S50. Simulations for haplotype width 2
Figure S51. Simulations for haplotype width 4
Figure S52. Simulations for haplotype width 6
Figure S53. Simulations for haplotype width 8
Figure S54. Simulations for haplotype width 10

Comparative power results between different intervals of disease mutation frequencies using samples of 500 trios, low relative risks

Figure S55. Simulations for haplotype width 1
Figure S56. Simulations for haplotype width 2
Figure S57. Simulations for haplotype width 4
Figure S58. Simulations for haplotype width 6
Figure S59. Simulations for haplotype width 8
Figure S60. Simulations for haplotype width 10

Real data

Figure S61 CTDT maps for window width of 1
Figure S62 CTDT maps for window width of 2
Figure S63 CTDT maps for window width of 4
Figure S64 CTDT maps for window width of 6
Figure S65 CTDT maps for window width of 8
Figure S66 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
README