Sib-pair Command: rare


ClassAnalysis and data manipulation command
Namerare
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

--------------------------------------------------
 Counts of rare alleles versus "trait"
--------------------------------------------------
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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