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3 dni temu · Sample-distance and similarity matrices. Relationship/covariance. --make-rel ['cov'] ['meanimpute'] [ {square | square0 | triangle}] [ {zs | bin | bin4}] --make-rel is the primary interface to PLINK's genetic relationship matrix and covariance matrix calculator.
3 dni temu · These matrices capture the pairwise dissimilarities or distances between objects, making PCoA particularly valuable in fields like ecology, genetics, and social sciences where relationships are often expressed as distances rather than direct measurements.
30 cze 2024 · Estimate genetic maps. Description. Uses a hidden Markov model to re-estimate the genetic map for an experimental cross, with possible allowance for genotyping errors. Usage. est_map( cross, error_prob = 0.0001, map_function = c("haldane", "kosambi", "c-f", "morgan"), lowmem = FALSE, maxit = 10000, tol = 0.000001, quiet = TRUE, save_rf = FALSE,
15 cze 2024 · This distance matrix algorithm computes pairwise distances between all points in a dataset, providing a comprehensive measure of similarity or dissimilarity. The algorithm constructs a square matrix where each element represents the distance between two points.
20 cze 2024 · Estimate phylogenetic diversity (PD), mean pairwise distance (MPD), and mean nearest taxon distance (MNTD). Description. Currently only non-abundance-weighted estimates are implemented. Usage phyloseq_phylo_div( physeq, measures = c("PD", "MPD", "MNTD", "SES.PD", "SES.MPD", "SES.MNTD"), ... ) Arguments
5 dni temu · I’ve closed out the prior discussion at Compute distance matrix - #9 by Linno but linking it here for context. This may still be a work in progress, but @bernt-matthias is the best person to answer. bernt-matthias July 5, 2024, 9:05pm 3. Dear @Linno. The reported values are the just the maximum number of common intervals for a gene order of ...
25 cze 2024 · Sparse distance matrix calculations. Description. Sparse alternative to base dist function. WARNING: the result is not a distance metric, see details! Also: distances are calculated between columns (not between rows, as in the base dist function). Usage. distSparse(M, method = "euclidean", diag = FALSE) Arguments. Details.
