importTaxpasta: Import taxpasta-specific BIOM results to...

In microbiome/mia: Microbiome analysis

Import taxpasta-specific BIOM results to TreeSummarizedExperiment

Description

Import taxpasta-specific BIOM results to TreeSummarizedExperiment

Usage

importTaxpasta(file, add.tree = TRUE, ...)

Arguments

file	Character scalar. Defines the file path to a BIOM file.
add.tree	Logical scalar. Specifies whether to calculate and add hierarchy tree using addHierarchyTree. (Default: TRUE)
...	additional arguments set.ranks: Logical scalar. Should column names of taxonomy table be treated as taxonomy ranks? (Default: FALSE)

Details

importTaxpasta imports data that is returned from Taxonomic Profile Aggregation and Standardization (taxpasta) pipeline. See more information on taxpasta from taxpasta documentation.

Value

A TreeSummarizedExperiment object.

See Also

importBIOM convertFromBIOM

Examples

## Not run: 
# File path to BIOM file
file_path <- system.file("extdata", "complete.biom", package = "mia")
# Import BIOM as TreeSE, and set ranks.
tse <- importTaxpasta(file_path, set.ranks = TRUE)
# Import BIOM as TreeSE without adding hierarchy tree
tse <- importTaxpasta(file_path, add.tree = FALSE)

## End(Not run)

microbiome/mia documentation built on Sept. 19, 2024, 11:17 p.m.