Zalpha: Runs the Zalpha function
In zalpha: Run a Suite of Selection Statistics

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	Zalpha(pos, ws, x, minRandL = 4, minRL = 25, X = NULL)

`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 `pos` vector.
`x`	A matrix of SNP values. Columns represent chromosomes; rows are SNP locations. Hence, the number of rows should equal the length of the `pos` vector. SNPs should all be biallelic.
`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 `c(startposition, endposition)`. The start position and the end position should be within the extremes of the positions given in the `pos` vector. If not supplied, the function will calculate Zalpha for every SNP in the `pos` vector.

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

## load the snps example dataset
data(snps)
## run Zalpha over all the SNPs with a window size of 3000 bp
Zalpha(snps$bp_positions,3000,as.matrix(snps[,3:12]))
## only return results for SNPs between locations 600 and 1500 bp
Zalpha(snps$bp_positions,3000,as.matrix(snps[,3:12]),X=c(600,1500))