detectFields: Detect metabData Input Columns

View source: R/detectFields.R

detectFieldsR Documentation

Detect metabData Input Columns

Description

This function ensures that metabolomics datasets used as inputs for the program possess all of the required fields, plus any optional columns that may appear in the final report table.

Usage

detectFields(Data, table, mz, rt, id, adduct, samples, extra, Q)

Arguments

Data

a metabData object.

table

data frame containing metabolomics features or path to metabolomics data file.

mz

Character name(s) / regular expressions associated with data column containing m/z values. The first column whose name contains this expression will be selected for analysis.

rt

Character name(s) / regular expression associated with data column containing retention time values. The first column whose name contains this expression will be selected for analysis.

id

Character name(s) or regular expression associated with data column containing metabolomics feature identifiers. The first column whose name contains this expression will be selected for analysis.

adduct

Character name(s) or regular expression associated with data column containing adduct, formula, or additional annotations. The first column whose name contains this expression will be selected for analysis.

samples

Character names of columns containing sample values. All numeric columns containing these keywords are selected for analysis. If no keywords given, searches for longest stretch of numeric columns remaining.

extra

Character names of columns containing additional feature information, e.g. non-analyzed sample values. All columns containing these keywords are selected for analysis.

Q

Character name(s) or regular expression associated with numeric feature abundance quantiles.

Value

an initialized and formatted metabData object.


hhabra/Combiner documentation built on Sept. 13, 2022, 11:34 a.m.