multi.spiec.easi: multi domain SPIEC-EASI

Description Usage Arguments Details See Also

View source: R/spiec-easi.R

Description

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

Usage

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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. 1, 2018, 2:12 p.m.