remove_features: Remove features based on different criteria

In szymczak-lab/preprocessHighResMS: Preprocessing of spectra data from high resolution mass spectrometry

Description

Remove features with no variability (method = "constant"), missing values (method = "missing"), low intensity (method = "zero") or identical peaks (method = "identical.peaks").

Usage

remove_features(se, assay, method, freq = 0.25, verbose = FALSE)

Arguments

se	RangedSummarizedExperiment-class object
assay	Character or integer. Name or number of assay to be used for filtering.
method	Method to determine features to be removed: "constant", "missing", "zero", "identical.peaks".
freq	Numeric. If more or equal than freq*100 criterion the feature is removed (not used if method = "constant").
verbose	Logical. Should number of removed features be reported?

Value

RangedSummarizedExperiment-class object with features removed

Examples

data("se.example")
se.example = remove_features(se = se.example,
                             assay = "mz",
                             method = "identical.peaks")

szymczak-lab/preprocessHighResMS documentation built on Oct. 6, 2020, 12:50 a.m.