snpmclust: Genotype clustering and calling
In SNPMClust: Bivariate Gaussian Genotype Clustering and Calling for Illumina Microarrays
Description
Usage
Arguments
Value
Author(s)
References
Examples
Description
Genotype clustering and calling for Illumina microarrays.
Usage
1
2
3
Arguments
indata
A list containing input data on one or all SNPs, and would normally be produced by the function prepdata. Details on the different components of indata can be seen in help(prepdata).
p
A positive integer specifying which SNP to cluster. The default is 1.
priorfrac
A non-negative scalar specifying the number of observations, as a fraction of the number of samples N, of pseudodata to be appended to the heterozygous and homozygous minor genotypes. The default is 0.2.
uncertcutoff
Genotype calls with uncertainty greater than uncertcutoff are set to "NC" (no call). The default is 0.01.
qcutoff
Uncertainty scores lower than the qcutoff'th quantile are reset to that value. When used with R.lowcutoff, this is equivalent to requiring a SNP-specific call rate of qcutoff or higher.
showplots
A logical value. If TRUE, the function will produce a series of plots. The default is FALSE.
xm1, xm2, xm3, ym1, ym2, ym3
Pseudodata cluster means can be user-specified through these parameters. The ordered pair (xm1,ym1) gives the cluster mean
for genotype AA; similarly for (xm2,ym2), (xm3,ym3) and AB, BB, respectively. Default values are NA, in which case cluster
means are estimated from the data, conditional on the a priori genotypes produced by GenomeStudio.
ranseed
Random seed for generation of pseudodata. The default is 1969.
R.lowcutoff
Genotypes for which R is less than R.lowcutoff are set to "NC" (no call). The default is 0.05.
Value
A list with the following components:
calls
A data frame with N rows and 4 columns, namely, SNP, SampleID, MClustCalls (the genotype call), and Uncertainty.
snp
The SNP name (i.e. rs-number).
callrate
Call rate for the SNP.
priorfrac
Value of argument in function call.
uncertcutoff
Value of argument in function call.
qcutoff
Value of argument in function call.
Author(s)
Stephen W. Erickson serickson@rti.org
with Joshua C. Callaway joshcllw@gmail.com
References
Stephen W. Erickson, Joshua Callaway (2016). SNPMClust: Bivariate Gaussian Genotype Clustering and Calling for Illumina Microarrays. Journal of Statistical Software, 71(2), 1-9. doi:10.18637/jss.v071.c02
Examples
1
2
3
Example output
Loading required package: MASS
Loading required package: mclust
Package 'mclust' version 5.3
Type 'citation("mclust")' for citing this R package in publications.
$calls
SNP SampleID MClustCalls Uncertainty
1 rs01 ID1 AB 8.250553e-05
2 rs01 ID2 AB 7.531890e-04
3 rs01 ID3 AA 6.888464e-09
4 rs01 ID4 AB 2.212727e-03
5 rs01 ID5 AA 3.805802e-07
6 rs01 ID6 AB 7.994968e-03
7 rs01 ID7 AB 9.664116e-03
8 rs01 ID8 AA 1.362355e-08
9 rs01 ID9 AB 1.524775e-05
10 rs01 ID10 AA 2.486900e-14
11 rs01 ID11 NC 1.405959e-02
12 rs01 ID12 AB 7.849124e-10
13 rs01 ID13 AA 2.241569e-05
14 rs01 ID14 AA 1.219025e-13
15 rs01 ID15 AA 1.634470e-12
16 rs01 ID16 BB 1.742131e-09
17 rs01 ID17 NC 2.457102e-02
18 rs01 ID18 AA 5.103112e-06
19 rs01 ID19 AA 3.064184e-05
20 rs01 ID20 AB 1.342320e-08
21 rs01 ID21 AA 6.721512e-12
22 rs01 ID22 AB 4.126413e-10
23 rs01 ID23 AB 6.474239e-10
24 rs01 ID24 AA 1.311191e-08
25 rs01 ID25 AB 5.710964e-03
26 rs01 ID26 BB 7.383474e-10
27 rs01 ID27 AB 1.756933e-09
28 rs01 ID28 AA 7.025491e-13
29 rs01 ID29 BB 3.064216e-14
30 rs01 ID30 NC 2.505060e-01
31 rs01 ID31 AB 8.175530e-03
32 rs01 ID32 AB 4.583016e-10
33 rs01 ID33 AB 1.412231e-09
34 rs01 ID34 AA 1.788515e-08
35 rs01 ID35 BB 4.397838e-11
36 rs01 ID36 AA 9.836576e-14
37 rs01 ID37 AA 1.323039e-10
38 rs01 ID38 AB 2.778449e-10
39 rs01 ID39 AA 1.067870e-04
40 rs01 ID40 AB 9.871720e-06
41 rs01 ID41 AA 2.984085e-09
42 rs01 ID42 AA 1.425333e-10
43 rs01 ID43 AB 6.274625e-11
44 rs01 ID44 BB 8.535345e-08
45 rs01 ID45 AA 3.321405e-06
46 rs01 ID46 AB 1.331396e-06
47 rs01 ID47 AA 1.483432e-04
48 rs01 ID48 NC 7.051057e-02
49 rs01 ID49 BB 1.109350e-04
50 rs01 ID50 AA 3.330669e-15
51 rs01 ID51 AB 3.572845e-08
52 rs01 ID52 AA 2.719770e-06
53 rs01 ID53 AB 2.520463e-09
54 rs01 ID54 AA 2.468914e-12
55 rs01 ID55 AB 9.647242e-09
56 rs01 ID56 AA 4.101541e-11
57 rs01 ID57 AB 2.599923e-06
58 rs01 ID58 AA 8.804615e-09
59 rs01 ID59 AB 4.178042e-10
60 rs01 ID60 AB 6.409481e-09
61 rs01 ID61 AA 3.596465e-07
62 rs01 ID62 AB 6.635912e-09
63 rs01 ID63 AB 2.186475e-10
64 rs01 ID64 AB 1.071703e-07
65 rs01 ID65 AB 8.165179e-07
66 rs01 ID66 AA 1.501073e-10
67 rs01 ID67 AA 2.090571e-09
68 rs01 ID68 NC 1.193337e-01
69 rs01 ID69 AA 2.746170e-10
70 rs01 ID70 AB 1.279008e-09
71 rs01 ID71 AA 1.778515e-04
72 rs01 ID72 AA 1.163156e-09
73 rs01 ID73 AA 1.084688e-12
74 rs01 ID74 BB 5.263789e-12
75 rs01 ID75 AA 1.977285e-10
76 rs01 ID76 AB 9.619148e-10
77 rs01 ID77 AA 4.658575e-08
78 rs01 ID78 AB 6.457019e-09
79 rs01 ID79 AA 1.157058e-05
80 rs01 ID80 BB 9.954704e-11
81 rs01 ID81 AB 3.557981e-10
82 rs01 ID82 AA 1.567247e-04
83 rs01 ID83 AA 2.449852e-08
84 rs01 ID84 AA 3.872950e-05
85 rs01 ID85 AA 1.301972e-09
86 rs01 ID86 AA 1.644960e-08
87 rs01 ID87 BB 2.043067e-08
88 rs01 ID88 AB 1.414779e-11
89 rs01 ID89 AA 6.048557e-07
90 rs01 ID90 AA 7.764938e-10
91 rs01 ID91 AA 3.623708e-09
92 rs01 ID92 AA 8.179109e-07
93 rs01 ID93 AA 2.927858e-11
94 rs01 ID94 AA 2.087616e-06
95 rs01 ID95 AB 1.660760e-09
96 rs01 ID96 AA 1.667555e-13
97 rs01 ID97 AB 1.202480e-10
98 rs01 ID98 AB 6.054492e-10
99 rs01 ID99 AA 6.324792e-07
100 rs01 ID100 BB 1.398881e-14
101 rs01 ID101 AA 6.349100e-09
102 rs01 ID102 AB 4.284191e-09
103 rs01 ID103 AA 1.512402e-06
104 rs01 ID104 AA 2.376782e-05
105 rs01 ID105 AA 6.322955e-10
106 rs01 ID106 AB 5.102299e-10
107 rs01 ID107 BB 3.330669e-14
108 rs01 ID108 AA 1.107515e-09
109 rs01 ID109 AA 1.623070e-08
110 rs01 ID110 AA 8.016754e-08
111 rs01 ID111 AA 4.462801e-05
112 rs01 ID112 AB 1.342390e-07
113 rs01 ID113 AA 8.089174e-11
114 rs01 ID114 BB 1.925518e-10
115 rs01 ID115 AB 3.048002e-09
116 rs01 ID116 AA 3.613341e-07
117 rs01 ID117 AB 1.308998e-09
118 rs01 ID118 AB 7.189954e-09
119 rs01 ID119 AB 3.683015e-07
120 rs01 ID120 AA 1.038469e-04
121 rs01 ID121 AA 7.329737e-11
122 rs01 ID122 BB 5.258460e-12
123 rs01 ID123 AA 1.474296e-09
124 rs01 ID124 AA 4.679994e-07
125 rs01 ID125 AA 1.968662e-09
126 rs01 ID126 AA 2.796501e-09
127 rs01 ID127 AA 3.585576e-12
128 rs01 ID128 AB 1.780765e-08
129 rs01 ID129 NC 1.961649e-02
130 rs01 ID130 AA 1.407046e-06
131 rs01 ID131 AB 4.999121e-06
132 rs01 ID132 AB 3.475893e-09
133 rs01 ID133 AA 1.451523e-07
134 rs01 ID134 AA 4.453675e-10
135 rs01 ID135 AB 1.273498e-09
136 rs01 ID136 AA 5.096151e-09
137 rs01 ID137 BB 5.986323e-13
138 rs01 ID138 AB 1.384206e-09
139 rs01 ID139 AB 5.549671e-08
140 rs01 ID140 AB 7.055974e-10
141 rs01 ID141 AB 3.883453e-04
142 rs01 ID142 AA 4.245518e-07
143 rs01 ID143 BB 1.185296e-11
144 rs01 ID144 BB 8.211209e-13
145 rs01 ID145 AA 5.656332e-08
146 rs01 ID146 BB 2.856604e-12
147 rs01 ID147 AB 5.825052e-09
148 rs01 ID148 AB 1.838179e-08
149 rs01 ID149 AB 3.974616e-09
150 rs01 ID150 AB 2.035772e-08
151 rs01 ID151 BB 7.940315e-13
152 rs01 ID152 AA 1.396964e-09
153 rs01 ID153 AB 2.329074e-09
154 rs01 ID154 AA 2.729972e-11
155 rs01 ID155 AA 7.809860e-08
156 rs01 ID156 AB 2.634896e-07
157 rs01 ID157 BB 2.034439e-11
158 rs01 ID158 AB 1.196386e-09
159 rs01 ID159 AA 1.975420e-11
160 rs01 ID160 AA 3.304179e-11
161 rs01 ID161 AA 1.516565e-13
162 rs01 ID162 AB 5.448797e-11
163 rs01 ID163 AA 6.501522e-10
164 rs01 ID164 AA 3.471781e-10
165 rs01 ID165 AA 2.501830e-09
166 rs01 ID166 AA 1.874723e-12
167 rs01 ID167 BB 1.476386e-10
168 rs01 ID168 BB 1.029554e-11
169 rs01 ID169 AA 1.216738e-11
170 rs01 ID170 AB 1.925544e-07
171 rs01 ID171 BB 8.707057e-09
172 rs01 ID172 AB 1.529284e-09
173 rs01 ID173 BB 1.869505e-11
174 rs01 ID174 AB 3.283307e-09
175 rs01 ID175 BB 2.580719e-06
176 rs01 ID176 AA 8.119949e-12
177 rs01 ID177 AA 9.827694e-13
178 rs01 ID178 AB 8.376635e-09
179 rs01 ID179 AA 1.313205e-10
180 rs01 ID180 AB 8.255923e-09
181 rs01 ID181 AA 1.034375e-07
182 rs01 ID182 BB 1.322720e-12
183 rs01 ID183 AB 1.798345e-09
184 rs01 ID184 AB 6.278113e-09
185 rs01 ID185 AB 3.599338e-07
186 rs01 ID186 BB 4.574119e-14
187 rs01 ID187 AB 1.764455e-07
188 rs01 ID188 AB 8.604886e-10
189 rs01 ID189 AA 8.668177e-12
190 rs01 ID190 AB 1.282514e-09
191 rs01 ID191 BB 8.006928e-13
192 rs01 ID192 AA 2.292582e-10
193 rs01 ID193 AA 1.356397e-08
194 rs01 ID194 AB 7.835908e-09
195 rs01 ID195 BB 1.450384e-10
196 rs01 ID196 AB 3.536585e-09
197 rs01 ID197 NC 1.336274e-02
198 rs01 ID198 AB 8.963931e-08
199 rs01 ID199 BB 1.940729e-09
200 rs01 ID200 AA 3.239410e-03
$snp
[1] "rs01"
$callrate
[1] 0.965
$priorfrac
[1] 0.2
$uncertcutoff
[1] 0.01
$qcutoff
[1] 0
SNPMClust documentation built on May 2, 2019, 2:44 a.m.
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Description Usage Arguments Value Author(s) References Examples
Description
Genotype clustering and calling for Illumina microarrays.
Usage
1 2 3 |
Arguments
indata |
A list containing input data on one or all SNPs, and would normally be produced by the function |
p |
A positive integer specifying which SNP to cluster. The default is 1. |
priorfrac |
A non-negative scalar specifying the number of observations, as a fraction of the number of samples N, of pseudodata to be appended to the heterozygous and homozygous minor genotypes. The default is 0.2. |
uncertcutoff |
Genotype calls with uncertainty greater than |
qcutoff |
Uncertainty scores lower than the |
showplots |
A logical value. If TRUE, the function will produce a series of plots. The default is FALSE. |
xm1, xm2, xm3, ym1, ym2, ym3 |
Pseudodata cluster means can be user-specified through these parameters. The ordered pair (xm1,ym1) gives the cluster mean for genotype AA; similarly for (xm2,ym2), (xm3,ym3) and AB, BB, respectively. Default values are NA, in which case cluster means are estimated from the data, conditional on the a priori genotypes produced by GenomeStudio. |
ranseed |
Random seed for generation of pseudodata. The default is 1969. |
R.lowcutoff |
Genotypes for which R is less than R.lowcutoff are set to "NC" (no call). The default is 0.05. |
Value
A list with the following components:
calls |
A data frame with N rows and 4 columns, namely, |
snp |
The SNP name (i.e. rs-number). |
callrate |
Call rate for the SNP. |
priorfrac |
Value of argument in function call. |
uncertcutoff |
Value of argument in function call. |
qcutoff |
Value of argument in function call. |
Author(s)
Stephen W. Erickson serickson@rti.org with Joshua C. Callaway joshcllw@gmail.com
References
Stephen W. Erickson, Joshua Callaway (2016). SNPMClust: Bivariate Gaussian Genotype Clustering and Calling for Illumina Microarrays. Journal of Statistical Software, 71(2), 1-9. doi:10.18637/jss.v071.c02
Examples
1 2 3 |
Example output
Loading required package: MASS
Loading required package: mclust
Package 'mclust' version 5.3
Type 'citation("mclust")' for citing this R package in publications.
$calls
SNP SampleID MClustCalls Uncertainty
1 rs01 ID1 AB 8.250553e-05
2 rs01 ID2 AB 7.531890e-04
3 rs01 ID3 AA 6.888464e-09
4 rs01 ID4 AB 2.212727e-03
5 rs01 ID5 AA 3.805802e-07
6 rs01 ID6 AB 7.994968e-03
7 rs01 ID7 AB 9.664116e-03
8 rs01 ID8 AA 1.362355e-08
9 rs01 ID9 AB 1.524775e-05
10 rs01 ID10 AA 2.486900e-14
11 rs01 ID11 NC 1.405959e-02
12 rs01 ID12 AB 7.849124e-10
13 rs01 ID13 AA 2.241569e-05
14 rs01 ID14 AA 1.219025e-13
15 rs01 ID15 AA 1.634470e-12
16 rs01 ID16 BB 1.742131e-09
17 rs01 ID17 NC 2.457102e-02
18 rs01 ID18 AA 5.103112e-06
19 rs01 ID19 AA 3.064184e-05
20 rs01 ID20 AB 1.342320e-08
21 rs01 ID21 AA 6.721512e-12
22 rs01 ID22 AB 4.126413e-10
23 rs01 ID23 AB 6.474239e-10
24 rs01 ID24 AA 1.311191e-08
25 rs01 ID25 AB 5.710964e-03
26 rs01 ID26 BB 7.383474e-10
27 rs01 ID27 AB 1.756933e-09
28 rs01 ID28 AA 7.025491e-13
29 rs01 ID29 BB 3.064216e-14
30 rs01 ID30 NC 2.505060e-01
31 rs01 ID31 AB 8.175530e-03
32 rs01 ID32 AB 4.583016e-10
33 rs01 ID33 AB 1.412231e-09
34 rs01 ID34 AA 1.788515e-08
35 rs01 ID35 BB 4.397838e-11
36 rs01 ID36 AA 9.836576e-14
37 rs01 ID37 AA 1.323039e-10
38 rs01 ID38 AB 2.778449e-10
39 rs01 ID39 AA 1.067870e-04
40 rs01 ID40 AB 9.871720e-06
41 rs01 ID41 AA 2.984085e-09
42 rs01 ID42 AA 1.425333e-10
43 rs01 ID43 AB 6.274625e-11
44 rs01 ID44 BB 8.535345e-08
45 rs01 ID45 AA 3.321405e-06
46 rs01 ID46 AB 1.331396e-06
47 rs01 ID47 AA 1.483432e-04
48 rs01 ID48 NC 7.051057e-02
49 rs01 ID49 BB 1.109350e-04
50 rs01 ID50 AA 3.330669e-15
51 rs01 ID51 AB 3.572845e-08
52 rs01 ID52 AA 2.719770e-06
53 rs01 ID53 AB 2.520463e-09
54 rs01 ID54 AA 2.468914e-12
55 rs01 ID55 AB 9.647242e-09
56 rs01 ID56 AA 4.101541e-11
57 rs01 ID57 AB 2.599923e-06
58 rs01 ID58 AA 8.804615e-09
59 rs01 ID59 AB 4.178042e-10
60 rs01 ID60 AB 6.409481e-09
61 rs01 ID61 AA 3.596465e-07
62 rs01 ID62 AB 6.635912e-09
63 rs01 ID63 AB 2.186475e-10
64 rs01 ID64 AB 1.071703e-07
65 rs01 ID65 AB 8.165179e-07
66 rs01 ID66 AA 1.501073e-10
67 rs01 ID67 AA 2.090571e-09
68 rs01 ID68 NC 1.193337e-01
69 rs01 ID69 AA 2.746170e-10
70 rs01 ID70 AB 1.279008e-09
71 rs01 ID71 AA 1.778515e-04
72 rs01 ID72 AA 1.163156e-09
73 rs01 ID73 AA 1.084688e-12
74 rs01 ID74 BB 5.263789e-12
75 rs01 ID75 AA 1.977285e-10
76 rs01 ID76 AB 9.619148e-10
77 rs01 ID77 AA 4.658575e-08
78 rs01 ID78 AB 6.457019e-09
79 rs01 ID79 AA 1.157058e-05
80 rs01 ID80 BB 9.954704e-11
81 rs01 ID81 AB 3.557981e-10
82 rs01 ID82 AA 1.567247e-04
83 rs01 ID83 AA 2.449852e-08
84 rs01 ID84 AA 3.872950e-05
85 rs01 ID85 AA 1.301972e-09
86 rs01 ID86 AA 1.644960e-08
87 rs01 ID87 BB 2.043067e-08
88 rs01 ID88 AB 1.414779e-11
89 rs01 ID89 AA 6.048557e-07
90 rs01 ID90 AA 7.764938e-10
91 rs01 ID91 AA 3.623708e-09
92 rs01 ID92 AA 8.179109e-07
93 rs01 ID93 AA 2.927858e-11
94 rs01 ID94 AA 2.087616e-06
95 rs01 ID95 AB 1.660760e-09
96 rs01 ID96 AA 1.667555e-13
97 rs01 ID97 AB 1.202480e-10
98 rs01 ID98 AB 6.054492e-10
99 rs01 ID99 AA 6.324792e-07
100 rs01 ID100 BB 1.398881e-14
101 rs01 ID101 AA 6.349100e-09
102 rs01 ID102 AB 4.284191e-09
103 rs01 ID103 AA 1.512402e-06
104 rs01 ID104 AA 2.376782e-05
105 rs01 ID105 AA 6.322955e-10
106 rs01 ID106 AB 5.102299e-10
107 rs01 ID107 BB 3.330669e-14
108 rs01 ID108 AA 1.107515e-09
109 rs01 ID109 AA 1.623070e-08
110 rs01 ID110 AA 8.016754e-08
111 rs01 ID111 AA 4.462801e-05
112 rs01 ID112 AB 1.342390e-07
113 rs01 ID113 AA 8.089174e-11
114 rs01 ID114 BB 1.925518e-10
115 rs01 ID115 AB 3.048002e-09
116 rs01 ID116 AA 3.613341e-07
117 rs01 ID117 AB 1.308998e-09
118 rs01 ID118 AB 7.189954e-09
119 rs01 ID119 AB 3.683015e-07
120 rs01 ID120 AA 1.038469e-04
121 rs01 ID121 AA 7.329737e-11
122 rs01 ID122 BB 5.258460e-12
123 rs01 ID123 AA 1.474296e-09
124 rs01 ID124 AA 4.679994e-07
125 rs01 ID125 AA 1.968662e-09
126 rs01 ID126 AA 2.796501e-09
127 rs01 ID127 AA 3.585576e-12
128 rs01 ID128 AB 1.780765e-08
129 rs01 ID129 NC 1.961649e-02
130 rs01 ID130 AA 1.407046e-06
131 rs01 ID131 AB 4.999121e-06
132 rs01 ID132 AB 3.475893e-09
133 rs01 ID133 AA 1.451523e-07
134 rs01 ID134 AA 4.453675e-10
135 rs01 ID135 AB 1.273498e-09
136 rs01 ID136 AA 5.096151e-09
137 rs01 ID137 BB 5.986323e-13
138 rs01 ID138 AB 1.384206e-09
139 rs01 ID139 AB 5.549671e-08
140 rs01 ID140 AB 7.055974e-10
141 rs01 ID141 AB 3.883453e-04
142 rs01 ID142 AA 4.245518e-07
143 rs01 ID143 BB 1.185296e-11
144 rs01 ID144 BB 8.211209e-13
145 rs01 ID145 AA 5.656332e-08
146 rs01 ID146 BB 2.856604e-12
147 rs01 ID147 AB 5.825052e-09
148 rs01 ID148 AB 1.838179e-08
149 rs01 ID149 AB 3.974616e-09
150 rs01 ID150 AB 2.035772e-08
151 rs01 ID151 BB 7.940315e-13
152 rs01 ID152 AA 1.396964e-09
153 rs01 ID153 AB 2.329074e-09
154 rs01 ID154 AA 2.729972e-11
155 rs01 ID155 AA 7.809860e-08
156 rs01 ID156 AB 2.634896e-07
157 rs01 ID157 BB 2.034439e-11
158 rs01 ID158 AB 1.196386e-09
159 rs01 ID159 AA 1.975420e-11
160 rs01 ID160 AA 3.304179e-11
161 rs01 ID161 AA 1.516565e-13
162 rs01 ID162 AB 5.448797e-11
163 rs01 ID163 AA 6.501522e-10
164 rs01 ID164 AA 3.471781e-10
165 rs01 ID165 AA 2.501830e-09
166 rs01 ID166 AA 1.874723e-12
167 rs01 ID167 BB 1.476386e-10
168 rs01 ID168 BB 1.029554e-11
169 rs01 ID169 AA 1.216738e-11
170 rs01 ID170 AB 1.925544e-07
171 rs01 ID171 BB 8.707057e-09
172 rs01 ID172 AB 1.529284e-09
173 rs01 ID173 BB 1.869505e-11
174 rs01 ID174 AB 3.283307e-09
175 rs01 ID175 BB 2.580719e-06
176 rs01 ID176 AA 8.119949e-12
177 rs01 ID177 AA 9.827694e-13
178 rs01 ID178 AB 8.376635e-09
179 rs01 ID179 AA 1.313205e-10
180 rs01 ID180 AB 8.255923e-09
181 rs01 ID181 AA 1.034375e-07
182 rs01 ID182 BB 1.322720e-12
183 rs01 ID183 AB 1.798345e-09
184 rs01 ID184 AB 6.278113e-09
185 rs01 ID185 AB 3.599338e-07
186 rs01 ID186 BB 4.574119e-14
187 rs01 ID187 AB 1.764455e-07
188 rs01 ID188 AB 8.604886e-10
189 rs01 ID189 AA 8.668177e-12
190 rs01 ID190 AB 1.282514e-09
191 rs01 ID191 BB 8.006928e-13
192 rs01 ID192 AA 2.292582e-10
193 rs01 ID193 AA 1.356397e-08
194 rs01 ID194 AB 7.835908e-09
195 rs01 ID195 BB 1.450384e-10
196 rs01 ID196 AB 3.536585e-09
197 rs01 ID197 NC 1.336274e-02
198 rs01 ID198 AB 8.963931e-08
199 rs01 ID199 BB 1.940729e-09
200 rs01 ID200 AA 3.239410e-03
$snp
[1] "rs01"
$callrate
[1] 0.965
$priorfrac
[1] 0.2
$uncertcutoff
[1] 0.01
$qcutoff
[1] 0
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