adjustData {metabCombiner} | R Documentation

## Process and Filter Metabolomics Feature Lists

### Description

`adjustData` contains a set of pre-analysis steps for processing LC-MS metabolomics feature tables individually

### Usage

    adjustData(Data, misspc, measure, rtmin, rtmax, zero, duplicate)

### Arguments

`Data` | a metabData object.
`misspc` | Numeric. Threshold missingness percentage for analysis.
`measure` | Character. Choice of central abundance measure; either "median" or "mean".
`rtmin` | Numeric. Minimum retention time for analysis.
`rtmax` | Numeric. Maximum retention time for analysis.
`zero` | Logical. Whether to consider zero values as missing.
`duplicate` | Ordered numeric pair (m/z, rt) tolerance parameters for duplicate feature search.

### Details

The pre-analysis adjustment steps include: 1) Restriction to a feature retention time range `rtmin` ≤ rt ≤ `rtmax` 2) Removal of features with a percent missingness exceeding `misspc` 3) Removal of duplicate metabolomics features.

After processing, abundance quantile (Q) values are calculated between 0 & 1 for the remaining features, as ranked by the `measure` argument, unless provided by the user.

### Value

Updated `metabData` object. The `data` field is processed by the listed steps and `stats` list updated to contain feature statistics.

### See Also

`metabData`: the constructor for metabData objects, `filterRT`: function for filtering by retention times, `findDuplicates`: function for finding duplicates

[Package metabCombiner version 1.2.2 Index]