| Class | Analysis and data manipulation command |
| Name | rare |
| Arguments | (<binary trait> | <marker>) <thresh> |
Pools rare alleles in all currently active markers below a given threshold allele frequency. If a trait is specified, lists carrier individuals by trait locus status, and provide table of number of alleles carried versus trait locus status, along with a contingency chi-square test. If a marker is specified, the genotypes for this are replaced by dummy genotypes representing the number of rare alleles carried by the individual ("1/1"=0, "1/2"=1, "2/2"=2 or more).
Example:
>> rare trait 0.005
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Counts of rare alleles versus "trait"
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Rare defined as MAF < 0.005000
Locus Individual Case Genotype Notes
rs1411 85923--8592303 Control A/G [T/C] A gene
...
Number of eligible loci = 89
Rare variants carried by individual
Case 0 1 2 3+
------- ------ ------ ------ ------
Case 1040 83 11 0
Control 11543 1013 106 28
Unknown 2 0 0 0
No. complete observations = 13824
LR contingency chi-square = 5.7
Degrees of freedom = 3
Asymptotic P-value = 0.1292
Empiric P-value = 0.1578 (13824000 MCMC iterations)
Trend chi-square = 0.96 (P=0.3272)
Summed rare allele counts:
Case Rare (Prop) Total
Case 105 (0.001769) 59358
Control 1331 (0.001222) 1088853
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