multi.spiec.easi: multi domain SPIEC-EASI

In zdk123/SpiecEasi: Sparse Inverse Covariance for Ecological Statistical Inference

multi domain SPIEC-EASI

Description

A SPIEC-EASI pipeline for inferring a sparse inverse covariance matrix within and between multiple compositional datasets, under joint sparsity penalty.

Usage

multi.spiec.easi(
  datalist,
  method = "glasso",
  sel.criterion = "stars",
  verbose = TRUE,
  pulsar.select = TRUE,
  pulsar.params = list(),
  ...
)

## S3 method for class 'list'
spiec.easi(data, ...)

Arguments

datalist	list of non-normalized count OTU/data tables (stored in a matrix, data.frame or phyloseq/otu_table) with samples on rows and features/OTUs in columns
method	estimation method to use as a character string. Currently either 'glasso' or 'mb' (meinshausen-buhlmann's neighborhood selection)
sel.criterion	character string specifying criterion/method for model selection. Accepts 'stars' and 'bstars' [default]
verbose	flag to show progress messages
pulsar.select	flag to perform model selection. Choices are TRUE/FALSE/'batch'
pulsar.params	list of further arguments to pulsar or batch.pulsar. See the documentation for pulsar.params.
...	further arguments to sparseiCov / huge
data	non-normalized count OTU/data table with samples on rows and features/OTUs in columns. Can also be list of phyloseq objects.

Details

Can also run spiec.easi on a list and S3 will dispatch the proper function.

See Also

spiec.easi

zdk123/SpiecEasi documentation built on Oct. 20, 2023, 6:49 a.m.