Add results from MGnifyR to HoloFoodR results

Usage

addMGnify(x, y, ...)

# S4 method for class 'SummarizedExperiment,MultiAssayExperiment'
addMGnify(
  x,
  y,
  exp.name1 = "metagenomic",
  exp.name2 = "metagenomic_amplicon",
  replace = TRUE,
  ...
)

# S4 method for class 'SummarizedExperiment,SummarizedExperiment'
addMGnify(x, y, ...)

# S4 method for class 'SummarizedExperiment,ANY'
addMGnify(x, y, id.col1 = "sample_biosample", id.col2 = "accession", ...)

Arguments

x: SummarizedExperiment. Results from MGnifyR::getResult().
y: MultiAssayExperiment or SummarizedExperiment or data.frame-like table. Results from HoloFoodR::getResult() or sample metadata from it.
...: optional arguments not used currently.
exp.name1: Character scalar. Specifies the name of experiment that will be added to y. (Default: "metagenomic")
exp.name2: Character scalar. Specifies the name of experiment from HoloFoodR results. This experiment is used to match IDs with MGnify data. (Default: "metagenomic_amplicon")
replace: Logical scalar. Whether to replace the template experiment. (Default: TRUE)
id.col1: Character scalar. Specifies the name of column from colData(x) that includes HoloFood identifiers. (Default: "sample_biosample")
id.col2: Character scalar. Specifies the name of column from colData(y[[exp.name2]]) that includes HoloFood identifiers. (Default: "accession")

Value

MultiAssayExperiment

Details

Metagenomic data is found in MGnify rather than HoloFoodR, and the two databases use different sample identifiers. However, MGnify's sample metadata includes references to the identifiers used in the HoloFood database, making it straightforward to convert sample IDs for alignment with HoloFood data. Despite this, HoloFood contains additional metadata not available in MGnify. Moreover, integrating data into a MultiAssayExperiment while maintaining accurate sample and system matches can be challenging.

This function is designed to simplify these tasks, enabling seamless integration of MGnify data with HoloFood data after retrieval from the database. You need only to input the returned data from MGnifyR::getResult() and HoloFoodR::getResult() functions.

Examples


if (FALSE) { # \dontrun{
# Get data from HoloFood database
mae <- HoloFoodR::getResult(
    salmon_sample_ids,
    use.cache = TRUE
)

# Get data from MGnify database
mg <- MgnifyClient(
    useCache = TRUE,
    cacheDir = ".MGnifyR_cache"
)
tse <- MGnifyR::getResult(
    mg,
    accession = mgnify_analyses_ids,
    get.func = FALSE
)

# Add MGnify data to HoloFood data
mae <- addMGnify(tse, mae)
} # }