1 / 17

Outline of Pooling Code

Outline of Pooling Code. Randomly assign p ools Pick number of mutated families Pick a scenario (0, 1, or 2) for each family ( p = .25, .50, .25 respectively) 0 randomly pick 1 parent and 0 siblings 1 randomly pick 1 parent and 1 sibling 2 randomly pick 1 parent and both siblings

glyn
Download Presentation

Outline of Pooling Code

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Outline of Pooling Code Randomly assign pools Pick number of mutated families Pick a scenario (0, 1, or 2) for each family (p = .25, .50, .25 respectively) 0 randomly pick 1 parent and 0 siblings 1 randomly pick 1 parent and 1 sibling 2 randomly pick 1 parent and both siblings Calculate overlap between pools containing true mutants (observed variation) father-sibling 1 overlap father-sibling 2 overlap mother-sibling 1 overlap mother-sibling 2 overlap Concatenate overlapping families eliminate duplicate families Contaminant families are overlapping families that are not a mutated family Set.seed(928) Number of families = 100 Number of mutated families = 5

  2. FATHER 12 89 27 38 4 41 74 80 92 82 79 48 29 49 20 40 34 77 51 22 88 44 35 87 47 50 85 9 100 55 2 76 91 6 33 3 1 31 11 5 28 57 66 17 19 13 62 43 94 64 65 61 21 36 32 69 30 98 96 18 56 99 97 60 84 46 14 90 59 83 63 86 54 26 42 95 25 72 75 78 16 73 23 52 45 8 10 81 7 24 39 68 67 71 58 37 70 93 15 53

  3. MOTHER 39 95 46 89 23 94 63 22 54 60 82 30 34 53 15 97 68 78 2 32 80 12 48 4 71 43 66 44 9 35 99 75 6 59 51 90 16 49 86 69 62 87 14 38 96 76 42 3 58 8 24 45 85 37 18 31 56 92 10 77 40 83 52 73 55 100 67 17 33 93 91 98 84 61 29 21 28 11 72 70 81 7 41 13 74 79 88 26 65 19 25 36 1 50 64 27 5 57 47 20

  4. SIBLING 1 15 9 82 96 94 85 97 59 53 17 60 86 64 48 83 32 91 10 62 11 37 73 12 63 39 44 29 52 67 76 77 92 89 6 50 22 38 7 28 75 69 41 72 5 49 99 98 88 65 8 19 47 95 78 45 51 81 87 80 93 34 31 90 21 20 74 61 55 100 2 23 24 35 36 42 56 66 70 25 16 68 79 14 4 13 40 57 33 43 71 54 1 58 18 26 46 84 30 3 27

  5. SIBLING 2 29 71 63 9 86 17 89 34 40 83 51 80 66 81 84 18 72 7 79 36 44 3 58 13 98 14 31 2 21 67 1 93 10 59 19 47 56 26 64 77 16 5 27 28 41 23 46 42 61 82 30 94 53 91 49 92 55 22 15 50 11 70 52 85 45 37 96 32 20 60 65 97 88 6 35 4 69 73 24 8 43 95 39 33 100 87 74 75 57 25 38 76 68 62 90 12 48 99 78 54

  6. Mutated Families Mutfams 90 27 89 98 44 Scenario 1 0 2 0 2 Sibling S2 --- S1 & S2 --- S1 & S2 Parent M M F M M

  7. Possible Families M 99 75 6 59 51 90 16 49 86 69 S2 38 76 68 62 90 12 48 99 78 54 Mother Sibling 2 39 95 46 89 23 94 63 22 54 60 82 30 34 53 15 97 68 78 2 32 80 12 48 4 71 43 66 44 9 35 99 75 6 59 51 90 16 49 86 69 62 87 14 38 96 76 42 3 58 8 24 45 85 37 18 31 56 92 10 77 40 83 52 73 55 100 67 17 33 93 91 98 84 61 29 21 28 11 72 70 81 7 41 13 74 79 88 26 65 19 25 36 1 50 64 27 5 57 47 20 29 71 63 9 86 17 89 34 40 83 51 80 66 81 84 18 72 7 79 36 44 3 58 13 98 14 31 2 21 67 1 93 10 59 19 47 56 26 64 77 16 5 27 28 41 23 46 42 61 82 30 94 53 91 49 92 55 22 15 50 11 70 52 85 45 37 96 32 20 60 65 97 88 6 35 4 69 73 24 8 43 95 39 33 100 87 74 75 57 25 38 76 68 62 90 12 48 99 78 54

  8. Possible Families M 25 36 1 50 64 27 5 57 47 20 Mother 39 95 46 89 23 94 63 22 54 60 82 30 34 53 15 97 68 78 2 32 80 12 48 4 71 43 66 44 9 35 99 75 6 59 51 90 16 49 86 69 62 87 14 38 96 76 42 3 58 8 24 45 85 37 18 31 56 92 10 77 40 83 52 73 55 100 67 17 33 93 91 98 84 61 29 21 28 11 72 70 81 7 41 13 74 79 88 26 65 19 25 36 1 50 64 27 5 57 47 20

  9. Possible Families F 12 89 27 38 4 41 74 80 92 82 S1 77 92 89 6 50 22 38 7 28 75 S2 29 71 63 9 86 17 89 34 40 83 15 9 82 96 94 85 97 59 53 17 60 86 64 48 83 32 91 10 62 11 37 73 12 63 39 44 29 52 67 76 77 92 89 6 50 22 38 7 28 75 69 41 72 5 49 99 98 88 65 8 19 47 95 78 45 51 81 87 80 93 34 31 90 21 20 74 61 55 100 2 23 24 35 36 42 56 66 70 25 16 68 79 14 4 13 40 57 33 43 71 54 1 58 18 26 46 84 30 3 27 29 71 63 9 86 17 89 34 40 83 51 80 66 81 84 18 72 7 79 36 44 3 58 13 98 14 31 2 21 67 1 93 10 59 19 47 56 26 64 77 16 5 27 28 41 23 46 42 61 82 30 94 53 91 49 92 55 22 15 50 11 70 52 85 45 37 96 32 20 60 65 97 88 6 35 4 69 73 24 8 43 95 39 33 100 87 74 75 57 25 38 76 68 62 90 12 48 99 78 54 Father Sibling 2 Sibling 1 12 89 27 38 4 41 74 80 92 82 79 48 29 49 20 40 34 77 51 22 88 44 35 87 47 50 85 9 100 55 2 76 91 6 33 3 1 31 11 5 28 57 66 17 19 13 62 43 94 64 65 61 21 36 32 69 30 98 96 18 56 99 97 60 84 46 14 90 59 83 63 86 54 26 42 95 25 72 75 78 16 73 23 52 45 8 10 81 7 24 39 68 67 71 58 37 70 93 15 53

  10. Possible Families M 91 98 84 61 29 21 28 11 72 70 Mother 39 95 46 89 23 94 63 22 54 60 82 30 34 53 15 97 68 78 2 32 80 12 48 4 71 43 66 44 9 35 99 75 6 59 51 90 16 49 86 69 62 87 14 38 96 76 42 3 58 8 24 45 85 37 18 31 56 92 10 77 40 83 52 73 55 100 67 17 33 93 91 98 84 61 29 21 28 11 72 70 81 7 41 13 74 79 88 26 65 19 25 36 1 50 64 27 5 57 47 20

  11. Possible Families M 80 12 48 4 71 43 66 44 9 35 S1 37 73 12 63 39 44 29 52 67 76 S2 44 3 58 13 98 14 31 2 21 67 15 9 82 96 94 85 97 59 53 17 60 86 64 48 83 32 91 10 62 11 37 73 12 63 39 44 29 52 67 76 77 92 89 6 50 22 38 7 28 75 69 41 72 5 49 99 98 88 65 8 19 47 95 78 45 51 81 87 80 93 34 31 90 21 20 74 61 55 100 2 23 24 35 36 42 56 66 70 25 16 68 79 14 4 13 40 57 33 43 71 54 1 58 18 26 46 84 30 3 27 29 71 63 9 86 17 89 34 40 83 51 80 66 81 84 18 72 7 79 36 44 3 58 13 98 14 31 2 21 67 1 93 10 59 19 47 56 26 64 77 16 5 27 28 41 23 46 42 61 82 30 94 53 91 49 92 55 22 15 50 11 70 52 85 45 37 96 32 20 60 65 97 88 6 35 4 69 73 24 8 43 95 39 33 100 87 74 75 57 25 38 76 68 62 90 12 48 99 78 54 Mother Sibling 1 39 95 46 89 23 94 63 22 54 60 82 30 34 53 15 97 68 78 2 32 80 12 48 4 71 43 66 44 9 35 99 75 6 59 51 90 16 49 86 69 62 87 14 38 96 76 42 3 58 8 24 45 85 37 18 31 56 92 10 77 40 83 52 73 55 100 67 17 33 93 91 98 84 61 29 21 28 11 72 70 81 7 41 13 74 79 88 26 65 19 25 36 1 50 64 27 5 57 47 20 Sibling 2

  12. Target Pools Father Mother 12 89 27 38 4 41 74 80 92 82 99 75 6 59 51 90 16 49 86 69 25 36 1 50 64 27 5 57 47 20 91 98 84 61 29 21 28 11 72 70 80 12 48 4 71 43 66 44 9 35 Sibling1 Sibling2 77 92 89 6 50 22 38 7 28 75 38 76 68 62 90 12 48 99 78 54 37 73 12 63 39 44 29 52 67 76 29 71 63 9 86 17 89 34 40 83 44 3 58 13 98 14 31 2 21 67

  13. Father and Sibling 1 Total Overlaps: 4 Father 12 89 27 38 4 41 74 80 92 82 Sibling1 77 92 89 6 50 22 387 28 75 37 73 12 63 39 44 29 52 67 76 Mutated Families: 90, 27, 89, 98, 44 Contaminant Families: 12, 38, 92

  14. Father and Sibling 2 Total Overlaps: 3 Father 12 89 2738 4 41 74 80 92 82 Sibling2 38 76 68 62 90 12 48 99 78 54 29 71 63 9 86 17 89 34 40 83 44 3 58 13 98 14 31 2 21 67 Mutated Families: 90, 27, 89, 98, 44 Contaminant Families: 12, 38

  15. Mother and Sibling 1 Total Overlaps: 7 Mother 99 75 6 59 51 90 16 49 86 69 25 36 1 5064 27 5 57 47 20 91 98 84 61 29 21 28 11 72 70 80 12 48 4 71 43 66 44 9 35 Sibling1 77 92 89 6 50 22 38 7 28 75 37 73 12 63 39 44 29 52 67 76 Mutated Families: 90, 27, 89, 98, 44 Contaminant Families: 75, 6, 50, 29, 28, 12

  16. Mother and Sibling 2 Total Overlaps: 11 Mother 99 75 6 59 51 90 16 49 86 69 25 36 1 50 64 27 5 57 47 20 9198 84 61 29 21 28 11 72 70 80 12 48 4 71 43 66 44 9 35 Sibling2 38 76 68 62 90 12 48 99 78 54 29 71 63 9 86 17 89 34 40 83 44 3 58 13 98 14 31 2 21 67 Mutated Families: 90, 27, 89, 98, 44 Contaminant Families: 99, 86, 29, 21, 12, 48, 71, 9

  17. OverlappingFamilies (18) Mutated Families (5) 6 9 12 21 28 29 38 44 48 50 71 75 86 89 90 92 98 99 90 27 89 98 44 Contaminant Families (14) 6 9 12 21 28 29 38 48 50 71 75 86 92 99

More Related