Calculate genetic distances

Usage

gen_dist(
  gen = NULL,
  dist_type = "euclidean",
  plink_file = NULL,
  plink_id_file = NULL,
  npc_selection = "auto",
  criticalpoint = 2.0234
)

Arguments

gen: path to vcf file, a vcfR type object, or a dosage matrix
dist_type: the type of genetic distance to calculate (options: "euclidean" (default), "bray_curtis", "dps" for proportion of shared alleles (requires vcf), "plink", or "pc" for PC-based)
plink_file: if "plink" dist_type is used, path to plink distance file (typically ".dist"; required only for calculating plink distance)
plink_id_file: if "plink" dist_type is used, path to plink id file (typically ".dist.id"; required only for calculating plink distance)
npc_selection: if dist_type = "pc", how to perform K selection (options: "auto" for automatic selection based on significant eigenvalues from Tracy-Widom test (default), or "manual" to examine PC screeplot and enter no. PCs into console)
criticalpoint: if dist_type = "pc" used with npc_selection = "auto", the critical point for the significance threshold for the Tracy-Widom test within the PCA (defaults to 2.0234 which corresponds to an alpha of 0.01)

Value

pairwise distance matrix for given distance metric

Details

Euclidean and Bray-Curtis distances calculated using the ecodist package: Goslee, S.C. and Urban, D.L. 2007. The ecodist package for dissimilarity-based analysis of ecological data. Journal of Statistical Software 22(7):1-19. DOI:10.18637/jss.v022.i07. Proportions of shared alleles calculated using the adegenet package: Jombart T. and Ahmed I. (2011) adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics. doi:10.1093/bioinformatics/btr521. For calculating proportions of shared alleles, missing values are ignored (i.e., prop shared alleles calculated from present values; no scaling performed)