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Import data into an mpactr object.

Source: R/import_data.R
import_data.Rd

import_data() takes two file paths, one for the pre-processed feature table and one for sample metadata. Both files should be .csv.

Usage

import_data(peak_table, meta_data, format = "none")

Arguments

peak_table

The file path or valid https url to your feature table file.

meta_data

The file path to your meta_data file or data.frame.

format

The expected exported type of your peak table, can be one of "Progenesis", "Metaboscape", "None".

Value

an mpactr_object.

Details

mpactr requires a peak table and meta data as input. Files are expected to be comma separated files (.csv).

  1. peak_table: a peak table where rows are expected to be compounds. mpactr supports import of feature table files from multiple tools through the format argument. Currently supported value for format are "Progenesis", "Metaboscape", or "None".

format = "Progensis" allows users to provide a feature table exported by Progenesis. To export a compatable peak table in Progenesis, navigate to the Review Compounds tab then File -> Export Compound Measurements. Select the following properties: Compound, m/z, Retention time (min), and Raw abundance and click ok.

format = "Metaboscape" allows users to provide a feature table exported by Metaboscape with default settings. The import function will save the raw peak table in the mpactr_object and store a formatted peak table for filtering. Reformatting includes selecting "FEATURE_ID", "RT", "PEPMASS", and sample columns. Sample columns are determined from the "Injection" column in meta_data (see below). "PEPMASS" is converted to m/z using the "ADDUCT" column and compound metadata columns are renamed for mpactr.

format = "None" allows users to provide a feature table file in the expected format. This can be useful if you have a file from another tool and want to manually format it in R. The table rows are expected to be individual features, while columns are compound metadata and samples. The feature table must have the compound metadata columns "Compound", "mz", and "rt". Where "Compound" is the compound id, and can be numeric or character. "mz" is the compound m/z, and should be numeric. "rt" is the retention time, in mintues, and should be numeric. The remaining columns should be samples, and match the names in the "Injection" column of the meta_data file. 2. meta_data: a table with sample information. Either a file path or data.frame can be supplied. At minimum the following columns are expected: "Injection", "Sample_Code", and "Biological_Group". "Injection" is the sample name and is expected to match sample column names in the peak_table. "Sample_Code" is the id for technical replicate groups. "Biological_Group" is the id for biological replicate groups. Other sample metadata can be added, and is encouraged for downstream analysis following filtering with mpactr.

Examples

data <- import_data(
  example_path("coculture_peak_table.csv"),
  example_path("metadata.csv"),
  format = "Progenesis"
)

meta_data <- read.csv(example_path("metadata.csv"))
data <- import_data(example_path("coculture_peak_table.csv"),
  meta_data,
  format = "Progenesis"
)