get_pairwise_correlations: Get all pairwise (MAP) correlations between microbes at...

In kimberlyroche/ROL: What the package does (short line)

Description

Get all pairwise (MAP) correlations between microbes at designated taxonomic level

Usage

get_pairwise_correlations(
  tax_level = "ASV",
  logratio = "alr",
  Sigmas = NULL,
  DLM = FALSE
)

Arguments

tax_level	taxonomic level at which to agglomerate data
logratio	logratio representation to use (e.g. "alr", "ilr", "clr")
Sigmas	optional list (indexed by host short name) of MAP estimates of microbial covariance; if not provided, this will be loaded
DLM	if TRUE, looks for DLM model fits instead of GP model fits
taxon_idx	the logratio coordinate to render correlations against

Value

correlation matrix of dimensions number of hosts x number of unique interactions between logratio taxa

Examples

interactions <- get_pairwise_correlations(tax_level = "ASV", logratio = "alr")

kimberlyroche/ROL documentation built on Dec. 10, 2020, 2:18 a.m.