R/applyFilt.R
gtest_filter.RdThe method identifies peptides, proteins, lipids, or metabolites to be filtered specifically according to the G-test.
gtest_filter(nonmiss_per_group, min_nonmiss_gtest, comparisons = NULL)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.
the minimum number of non-missing peptide values allowed in a minimum of one group. Default value is 3.
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.
filter.peps a character vector of the peptides to be filtered out prior to the G-test or IMD-ANOVA
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.