FilterVariable: Methods for non-specific filtering of variables

In xia-lab/MetaboAnalystR: An R Package for Comprehensive Analysis of Metabolomics Data

Methods for non-specific filtering of variables

Description

This is a function that filters the dataset, dependent on the user-specified method for filtering. The function applies a filtering method, ranks the variables within the dataset, and removes variables based on its rank. The final dataset should contain no more than than 5000 variables for effective computing.

Usage

FilterVariable(mSetObj=NA, filter, qcFilter, rsd)

Arguments

mSetObj	Input the name of the created mSetObj (see InitDataObjects)
qc.filter	Filter the variables based on QC samples - True (T), or use non-QC based filtering - False (F).
rsd	Define the relative standard deviation cut-off. Variables with a RSD greater than this number will be removed from the dataset. It is only necessary to specify this argument if qc.filter is True (T). Otherwise, it will not be used in the function.
var.filter	Select the filter option, "rsd" which is the relative standard deviation, "nrsd" which is the non-parametric relative standard deviation, "mean" which is the mean, "sd" which is the standard deviation, "mad" which is the median absolute deviation, or "iqr" which is the interquantile range.
var.cutoff	var.cutoff value
int.filter	int.filter value
int.cutoff	int.cutoff value, numeric
filter.cutoff	percent to be filtered, for example, 5 (5%)

Author(s)

Jeff Xia [e-mail] McGill University, Canada License: GNU GPL (>= 2)

xia-lab/MetaboAnalystR documentation built on Sept. 12, 2024, 2:23 p.m.