analyseTaxaInA: Compute edge statistics for an interaction matrix with...

In hallucigenia-sparsa/seqtime: Time Series Analysis of Sequencing Data

Compute edge statistics for an interaction matrix with taxonomic information

Description

The function expects an interaction matrix with taxon names given as row and column names and their assignment to a higher taxonomic level given in the first column (can be generated with assignTaxonLevelsToA). Either the edge number or the p-value of the edge number given the number of taxa in both higher-level taxon groups is reported. The p-value is computed by randomizing the interaction matrix while preserving the total number of its entries. Entries (i,j) and (j,i) in the interaction matrix are counted as one interaction by default.

Usage

analyseTaxaInA(taxonA, count.entries = FALSE, count.loops = FALSE,
  report.pval = FALSE, report.rand = FALSE, pos.only = FALSE,
  neg.only = FALSE, iters = 100, p.threshold = 0.05, sig = FALSE)

Arguments

taxonA	an interaction matrix with taxonomy (first column contains higher-level taxa)
count.entries	instead of interactions, count links (so entries (i,j) and (j,i) are not combined, but counted separately)
count.loops	count link of a node to itself
report.pval	if true, entries in the resulting interaction matrix are p-values of edge number between taxonomic groups, else edge numbers
report.rand	return the mean number of links found in randomized matrices
pos.only	only consider positive entries in taxonA
neg.only	only consider negative entries in taxonA
iters	number of randomizations for report.pval
p.threshold	only report higher-level links with p-values below given threshold
sig	convert p-values into significances

Value

an interaction matrix with as many rows and columns as there are distinct higher-level taxa in the first column of the input

Examples

data("david_stool_lineages")
# make a random OTU interaction matrix as an example
N=30
A=generateA(N=N,c=0.1)
randomOTUIndices=sample(1:nrow(david_stool_lineages))[1:N]
rownames(A)=david_stool_lineages[randomOTUIndices,1]
colnames(A)=rownames(A)
A.otu=assignTaxonLevelsToA(A,lineages=david_stool_lineages, taxon.level="genus",no.merge=TRUE)
A.phylum=analyseTaxaInA(A.otu,count.loops=TRUE, count.entries=TRUE)

hallucigenia-sparsa/seqtime documentation built on Jan. 9, 2023, 11:53 p.m.