prepInput: Create a SummarizedExperiment object

In biobakery/Macarron: Prioritization of potentially bioactive metabolic features from epidemiological and environmental metabolomics datasets

Create a SummarizedExperiment object

Description

Create a SummarizedExperiment object

Usage

prepInput(input_abundances, input_annotations, input_metadata)

Arguments

input_abundances	a dataframe (features x samples) containing metabolic feature intensities (abundances).
input_annotations	a dataframe (features x annotations) containing the available feature annotations. ^^Column 1 must contain standard annotations such as HMDB ID or Pubchem CID for the subset of identified/annotated features. ^^Column 2 must contain metabolite name. ^^Column 3 must contain a continuous numeric chemical property such as m/z or shift/ppm.
input_metadata	a dataframe (samples x metadata) containing sample metadata. ^^Row names must identify samples. ^^Column 1 must identify phenotypes or conditions (categorical metadata) associated with the samples. Must not contain NA. Rows with no specified phenotype/condition will be removed.

Value

SummarizedExperiment object

Examples

prism_abundances = system.file("extdata", "demo_abundances.csv", package="Macarron")
abundances_df = read.csv(file = prism_abundances, row.names = 1)
prism_annotations = system.file("extdata", "demo_annotations.csv", package="Macarron")
annotations_df = read.csv(file = prism_annotations, row.names = 1)
prism_metadata = system.file("extdata", "demo_metadata.csv", package="Macarron")
metadata_df = read.csv(file = prism_metadata, row.names = 1)
mbx <- Macarron::prepInput(input_abundances = abundances_df,
                            input_annotations = annotations_df,
                            input_metadata = metadata_df)

biobakery/Macarron documentation built on June 29, 2024, 7:58 a.m.