Description Usage Arguments Value References Examples
Returns a Zalpha value for each SNP location supplied to the function. For more information about the Zalpha statistic, please see Jacobs (2016). The Zalpha statistic is defined as:
Z_{α}=\frac{{|L| \choose 2}^{-1}∑_{i,j \in L}r^2_{i,j} + {|R| \choose 2}^{-1}∑_{i,j \in L}r^2_{i,j}}{2}
where |L|
and |R|
are the number of SNPs to the left and right of the current locus within the given window ws
, and r^2 is equal to the squared correlation between a pair of SNPs
1 |
pos |
A numeric vector of SNP locations |
ws |
The window size which the Zalpha statistic will be calculated over. This should be on the same scale as the |
x |
A matrix of SNP values. Columns represent chromosomes; rows are SNP locations. Hence, the number of rows should equal the length of the |
minRandL |
Minimum number of SNPs in each set R and L for the statistic to be calculated. Default is 4. |
minRL |
Minimum value for the product of the set sizes for R and L. Default is 25. |
X |
Optional. Specify a region of the chromosome to calculate Zalpha for in the format |
A list containing the SNP positions and the Zalpha values for those SNPs
Jacobs, G.S., T.J. Sluckin, and T. Kivisild, Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps. Genetics, 2016. 203(4): p. 1807
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