gtest_filter {pmartR}

Identifies peptides to be filtered out in preparation for IMD-ANOVA.

Description

The method identifies peptides, proteins, lipids, or metabolites to be filtered specifically according to the G-test.

Usage

gtest_filter(nonmiss_per_group, min_nonmiss_gtest, comparisons = NULL)

Arguments

nonmiss_per_group

list created by nonmissing_per_group. The first element giving the total number of possible samples for each group. The second element giving a data.frame with the first column giving the biomolecule and the second through kth columns giving the number of non-missing observations for each of the k groups.

min_nonmiss_gtest

the minimum number of non-missing peptide values allowed in a minimum of one group. Default value is 3.

comparisons

data.frame with columns for "Control" and "Test" containing the different comparisons of interest. Comparisons will be made between the Test and the corresponding Control. If left NULL, then all pairwise comparisons are executed.

Details

Two methods are available for determining the peptides to be filtered. The naive approach is based on min.nonmiss.allowed, and looks for peptides that do not have at least min.nonmiss.allowed values per group. The other approach also looks for peptides that do not have at least a minimum number of values per group, but this minimum number is determined using the G-test and a p-value threshold supplied by the user. The G-test is a test of independence, used here to test the null hypothesis of independence between the number of missing values across groups.

Value

filter.peps a character vector of the peptides to be filtered out prior to the G-test or IMD-ANOVA

Author(s)

Kelly Stratton