getClusterMemberCooccurrence: Retrieving member allele co-occurrence status and strain...

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

Retrieving member allele co-occurrence status and strain distributions for clusters of alleles

Description

This function returns a data frame given a data frame of cluster IDs and alleles. In each row, a string of strain names (comma-delimited) are returned if all of the alleles are co-occurring in these strains, otherwise, an NA is returned because alleles may differ in strains when only a fixed number (less than the number of all alleles) of alleles are co-occurring in the strains. Moreover, the function reports the minimal inclusive clade of strains and the frequency of co-occurrence events in this clade when all alleles are co-occurring.

Specifically, a cluster may refer to a community (also known as a module) or a clique in a network.

Usage

getClusterMemberCooccurrence(
  clstr,
  cluster.colname = "cluster",
  allele.colname = "allele",
  pam,
  clade.pam = NULL,
  clade.sizes = NULL,
  sample.dists = NULL,
  n.cores = -1
)

Arguments

clstr	a data frame consisting of at least two columns: one for cluster IDs and the other for allele names (comma-delimited). I recommend to use integers or characters as clster IDs. This argument can be generated by taking the columns Clique and Alleles in the output of the function summariseCliques.
cluster.colname	the column name for cluster IDs in clstr.
allele.colname	the column name for allele IDs in clstr.
pam	an allelic PAM with columns for allele names and rows for strain names.
clade.pam	(optional) a matrix for the presence/absence of samples in each clade of an input tree. It can be obtained using the function tree2Clades.
clade.sizes	(optional) A named vector of integers for the number of samples in each clade. It can be obtained from the element "sizes" in the outputs of the function tree2Clades. Optional.
sample.dists	(optional) A square matrix for distances between samples. It can be acquired through the function projectSamples.
n.cores	An integer determining the number of cores used for parallel computing. Valid values are the same as those for the function findPhysLink.

Value

A data frame of 12 columns. Explanations to some columns: Column 1, named by the argument cluster.colname, which contains cluster IDs; Column 2, named by the argument allele.colname, which stores alleles per cluster; size, number of alleles per cluster; co_max, maximum number of co-occurring alleles in strains; co_perc, co_max / size * 100

Note

Clade-wise summaries are not returned or only a few summary columns are returned when the three optional arguments are incomplete (some may be NULL).

Author(s)

Yu Wan ([e-mail])

Examples

assoc <- findPhysLink(...)
clusters <- ...  # from a network package of your preference
com.co <- getClusterMemberCooccurrence(com = clusters, pam = assoc[["alleles"]][["A"]], cluster.colname = "community",
clade.pam = assoc[["struc"]][["clades"]][["pam"]], clade.sizes = assoc[["struc"]][["clades"]][["sizes"]],
sample.dists = assoc[["struc"]][["C"]][["d"]], n.cores = 2)

Dependency: data.table, parallel

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