graph_perm_test {phyloseqGraphTest}

Performs graph-based permutation tests

Description

Performs graph-based tests for one-way designs.

Usage

graph_perm_test(
  physeq,
  sampletype,
  grouping = 1:nsamples(physeq),
  distance = "jaccard",
  type = c("mst", "knn", "threshold.value", "threshold.nedges"),
  max.dist = 0.4,
  knn = 1,
  nedges = nsamples(physeq),
  keep.isolates = TRUE,
  nperm = 499
)

Arguments

physeq

A phyloseq object.

sampletype

A string giving the column name of the sample to be tested. This should be a factor with two or more levels.

grouping

Either a string with the name of a sample data column or a factor of length equal to the number of samples in physeq. These are the groups of samples whose labels should be permuted and are used for repeated measures designs. Default is no grouping (each group is of size 1).

distance

A distance, see distance for a list of the possible methods.

type

One of "mst", "knn", "threshold". If "mst", forms the minimum spanning tree of the sample points. If "knn", forms a directed graph with links from each node to its k nearest neighbors. If "threshold", forms a graph with edges between every pair of samples within a certain distance.

max.dist

For type "threshold", the maximum distance between two samples such that we put an edge between them.

knn

For type "knn", the number of nearest neighbors.

nedges

If using "threshold.nedges", the number of edges to use.

keep.isolates

In the returned network, keep the unconnected points?

nperm

The number of permutations to perform.

Value

A list with the observed number of pure edges, the vector containing the number of pure edges in each permutation, the permutation p-value, the graph used for testing, and a vector with the sample types used for the test.

Examples

library(phyloseq)
data(enterotype)
gt = graph_perm_test(enterotype, sampletype = "SeqTech", type = "mst")
gt