allelicCoMatrix: Create a co-occurrence matrix from allelic PAM

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

Create a co-occurrence matrix from allelic PAM

Description

Create a co-occurrence matrix from allelic PAM

Usage

allelicCoMatrix(
  clusters = NULL,
  pam = NULL,
  hclust.method = NULL,
  hclust.dist = "binary"
)

Arguments

clusters	A named or unnamed list of allele name vectors that define alleles of each cluster. Every vector must contain at least two alleles.
pam	An allelic presence-absence matrix, where 1 denotes presence of an allele and 0 denotes absence of an allele.
hclust.method	Method for clustering columns in the output co-occurrence matrix. Default: NULL (no clustering)
hclust.dist	Distance metric used for column-wise clustering. Default: binary.

Value

A list of elements: m, a co-occurrence matrix; c, clusters, recordered if hclust.method != NULL; g: a vector (method, dist) for arguments of column-wise clustering (grouping).

Note

hclust.method and hclust.dist are passed to R base functions hclust and dist as arguments.

Author(s)

Yu Wan ([e-mail])

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