adjustData: Process and Filter Metabolomics Feature Lists

View source: R/adjustData.R

adjustDataR 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 \le rt \le rtmax 2) Removal of features with missingness percentage 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, filterRT


hhabra/Combiner documentation built on Jan. 26, 2024, 10:30 p.m.