getTopLoc | R Documentation |
getTopLoc
Extracts the genotypes of individuals at the top n (by Fst) "unlinked" loci. The loci returned are in linkage equilibrium above a user defined r^2 threshold. The resultant file can then be used to simulate the panel efficacy using freqbasedsim. Alternatively, multiple panel sizes can be created by using truncated vectors of the exported loci names in the function subset_genepop from the genepopedit package (www.github.com/rystanley)
getTopLoc(GPD, LDpop = "Pop1", panel.size, FST.threshold = 0.05,
allocate.PGD.RAM = 1, r2.threshold = 0.2, ld.window = NULL, where.PLINK,
where.PGDspider, return.environment = TRUE,
save.LociandIndividuals = FALSE)
GPD |
A file path to the GENEPOP format file you wish to create your panel from |
LDpop |
A string which denotes which of the two populations you wish to calculate linkage disequilibrium in. The options are "Pop1" or "Pop2", or "Both" if the LD is to be calculated based on both populations. |
panel.size |
An integer number of loci to include in the panel |
FST.threshold |
The minimum FST threshold required to retain a locus |
allocate.PGD.RAM |
An integer value in GB to specify the maximum amount of RAM to allocate to PGDspider. The default is 1 GB, which should be sufficient for most analyses. |
r2.threshold |
The minimum r^2 threshold to consider a pair of loci to be in LD |
ld.window |
Number of adjacent SNPs to compare each SNP against for LD - default is NULL, which translates to a window size of 99999, which essentially asks to compare each SNP against all others |
where.PLINK |
A file path to the PLINK installation folder |
where.PGDspider |
A file path to the PGDspider installation folder |
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.