retrieveAlleleSetInfo: Retrive allelic presence-absence information given a vector...

In wanyuac/GeneMates: Analysing association and physical linkage between bacterial genes

Retrive allelic presence-absence information given a vector of allele names

Description

This function is to be run after the findPhysLink pipeline.

Usage

retrieveAlleleSetInfo(
  targets,
  assoc,
  allelic.pam,
  min.count = 2,
  phylo.dists = NULL,
  dist.method = "binary",
  clust.method = "single"
)

Arguments

targets	A character vector of allele names whose co-occurrence information is to be retrieved
assoc	The element "assoc" in the output of findPhysLink.
allelic.pam	The element "assoc$A" in the output of findPhysLink.
min.count	(>= 1) The minimal number of alleles that an isolate must carry to be included in the extracted information
phylo.dists	A matrix of phylogenetic distances between tips of a tree. It can be generated using the function cophenetic.phylo(tree).
dist.method	The parameter for the method argument of the base function dist
clust.method	The parameter for the method argument of the base function hclust

Author(s)

Yu Wan ([e-mail])

Examples

retrieveAlleleSetInfo(targets = c("aadA2", "dfrA12", "sul1"), assoc = a[["assoc"]], allelic.pam = a[["alleles"]][["A"]], min.count = 2, phylo.dists = cophenetic.phylo(tr))

wanyuac/GeneMates documentation built on Aug. 12, 2022, 7:37 a.m.