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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

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Outline of pooling code
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


Father
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


Mother
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


Sibling 1
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


Sibling 2
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


Mutated families
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


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


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


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


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


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


Target pools
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


Father and sibling 1
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


Father and sibling 2
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


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


Mother and sibling 2
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


Overlapping families 18
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


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