imdanova_filter: IMD-ANOVA Filter Object

In pmartR/pmartR: Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data

IMD-ANOVA Filter Object

Description

This function returns an imdanovaFilt object for use with applyFilt

Usage

imdanova_filter(omicsData)

Arguments

omicsData

object of one of the classes "pepData", "isobaricpepData", "proData", "lipidData", "metabData", or "nmrData", created by as.pepData, as.isobaricpepData, as.proData, as.lipidData, as.metabData, or as.nmrData, respectively. Groups (more than one) must have been specified using the group_designation function prior to using the imdanova_filter function.

Details

The output from this function can be used in conjunction with applyFilt to filter out molecules that are not present in enough samples to do statistical comparisons. If any singleton groups are present in the omicsData object, those groups are not part of the filter object that is returned.

Value

An S3 object of class imdanovaFilt (also a data.frame) containing the molecule identifier and number of samples in each group with non-missing values for that molecule.

Author(s)

Kelly Stratton

Examples

library(pmartRdata)
mypep <- group_designation(omicsData = pep_object, main_effects = "Phenotype")
to_filter <- imdanova_filter(omicsData = mypep)
summary(to_filter, min_nonmiss_anova = 2)

pmartR/pmartR documentation built on March 4, 2024, 8:32 a.m.