spiec.easi: SPIEC-EASI pipeline

Description Usage Arguments See Also

View source: R/spiec-easi.R

Description

Run the whole SPIEC-EASI pipeline, from data transformation, sparse inverse covariance estimation and model selection. Inputs are a non-normalized OTU table and pipeline options.

Usage

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spiec.easi(data, ...)

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

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

## Default S3 method:
spiec.easi(data, method = "glasso",
  sel.criterion = "stars", verbose = TRUE, pulsar.select = TRUE,
  pulsar.params = list(), icov.select = pulsar.select,
  icov.select.params = pulsar.params, ...)

Arguments

data

For a matrix, non-normalized count OTU/data table with samples on rows and features/OTUs in columns. Can also by phyloseq or otu_table object.

...

further arguments to sparseiCov / huge

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' [default], 'bstars' (Bounded StARS)

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.

icov.select

deprecated.

icov.select.params

deprecated.

See Also

multi.spiec.easi


zdk123/SpiecEasi documentation built on Oct. 1, 2018, 2:12 p.m.