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

View source: R/func__retrieveAlleleSetInfo.R

retrieveAlleleSetInfoR Documentation

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 (wanyuac@126.com)

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.