A Tool for 'Covariate'-Sensitive Longitudinal Analysis on 'omics' Data

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Documentation for package ‘LongDat’ version 1.1.3

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

cliff_cal	Effect size (Cliff's delta) calculation in longdat_disc() pipeline
ConModelTest_cont	Covariate model test in longdat_cont() pipeline
ConModelTest_disc	Covariate model test in longdat_disc() pipeline
correlation_posthoc	Post-hoc test based on correlation test for longdat_cont().
cuneiform_plot	Create cuneiform plots of result table from longdat_disc() or longdat_cont()
data_preprocess	Data preprocessing
factor_p_cal	Calculate the p values for every factor (used for selecting factors later)
final_result_summarize_cont	Generate result table as output in longdat_cont()
final_result_summarize_disc	Generate result table as output in longdat_disc()
fix_name_fun	Replace the symbols in variable and covariate names in raw input
longdat_cont	Longitudinal analysis with time as continuous variable
LongDat_cont_feature_table	data/LongDat_cont_feature_table.RData documentation
LongDat_cont_master_table	data/LongDat_cont_master_table.RData documentation
LongDat_cont_metadata_table	data/LongDat_cont_metadata_table.RData documentation
longdat_disc	Longitudinal analysis with time as discrete variable
LongDat_disc_feature_table	data/LongDat_disc_feature_table.RData documentation
LongDat_disc_master_table	data/LongDat_disc_master_table.RData documentation
LongDat_disc_metadata_table	data/LongDat_disc_metadata_table.RData documentation
make_master_table	Create input master table from metadata and feature tables for longdat_disc() and longdat_cont()
NuModelTest_cont	Null Model Test and post-hoc Test in longdat_cont() pipeline
NuModelTest_disc	Null Model Test and post-hoc Test in longdat_disc() pipeline
random_neg_ctrl_cont	Randomized negative control for count data in longdat_cont()
random_neg_ctrl_disc	Randomized negative control for count data in longdat_disc()
rm_sparse_cont	Remove the dependent variables that are below the threshold of sparsity when the data type is count data in longdat_cont()
rm_sparse_disc	Remove the dependent variables that are below the threshold of sparsity when the data type is count data in longdat_disc()
theta_plot	Plot theta values of negative binomial models versus non-zero count for count data
unlist_table	Unlist confound (covariate) and inverse confound (covariate) tables, turn them into tables
wilcox_posthoc	Wilcoxon post-hoc test