Import TreeSummarizedExperiment

Import data from TreeSummarizedExperiment to MbioDataset. There is some loss of granularity in this process. It results in a simpler and more performant object which is compliant with the MicrobiomeDB infrastructure.

Usage

importTreeSummarizedExperiment(
  data,
  normalizationMethod = c("TSS", "none"),
  keepRawValues = c(TRUE, FALSE),
  verbose = c(TRUE, FALSE)
)

importTreeSE(
  data,
  normalizationMethod = c("TSS", "none"),
  keepRawValues = c(TRUE, FALSE),
  verbose = c(TRUE, FALSE)
)

Arguments

data

A TreeSummarizedExperiment

normalizationMethod

Normalization method to use on they assay data. Options are "none" and "TSS". Applying TSS normalization to absolute taxonomic abundances produces relative taxonomic abundances. Default is "TSS".

keepRawValues

Keep the raw assay values as well as the normalized values.

verbose

Print messages

Value

A MbioDataset

Examples

data(GlobalPatterns, package="mia")
tse <- GlobalPatterns

## no normalization, with raw values
mbioDataset <- importTreeSummarizedExperiment(
     tse, 
     normalizationMethod = "none", 
     keepRawValues = TRUE, 
     verbose = TRUE
)

## TSS normalization, drop raw values
mbioDataset <- importTreeSummarizedExperiment(
     tse, 
     normalizationMethod = "TSS", 
     keepRawValues = FALSE, 
     verbose = TRUE
)

## TSS normalization, keep raw values
mbioDataset <- importTreeSummarizedExperiment(
     tse, 
     normalizationMethod = "TSS", 
     keepRawValues = TRUE, 
     verbose = TRUE
)