tTestWithErrorHandling: This chunk of code is from EDec paper Select informative loci...

In bozdaglab/CTDPathSim2.0: Computing multi-omics driven similarity scores between patient tumor samples and cell lines for personalized medicine

This chunk of code is from EDec paper Select informative loci (EDec stage 0)

Description

run_edec_stage_0 selects loci/probes that display cell type specific patterns of methylation, and are likely to be informative for deconvolution. This selection is based on comparison of reference methylation profiles representing different cell types.

Usage

tTestWithErrorHandling(x)

Details

There are two versions of this method. The user can choose which one to use by setting the version argument to either "one.vs.rest" (default) or "each.pair". In the first version, the method will perform two-sample T-tests to compare the levels of methylation on each locus/probe between references of one class against all other references. These comparisons will be done for each reference class in turn. The method will then select the most hyper- and hypo-methylated loci/probes that showed p-value less than or equal to max_p_value. The same number of markers will be selected from each comparison, adding up to num_markers. The difference between the "one.vs.rest" version and the "each.pair" version of the method is that, instead of comparing one class of references against all others as is done in "one.vs.rest" version, the "each.pair" version will perform comparisons between each pair of reference classes.

p_1, data_group_2)

bozdaglab/CTDPathSim2.0 documentation built on April 14, 2022, 12:39 a.m.