Cell Explanatory Power with Inflection Point (CEP-IP) with CMRF

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Documentation for package ‘cepip’ version 0.1.0

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

Help Pages

cepip	Run CEP-IP, optionally with SKCS and CMRF
cepip_associate	Donor-level association with outcomes
cepip_band	CMRF tolerance band (Stage 1)
cepip_cmrf	Copula monotone recovery filter (CMRF)
cepip_composite	Composite expression of partner genes
cepip_deg	Differential expression between cell groups, paired by donor
cepip_donor	Per-donor share of cells in each group
cepip_ep	Cell explanatory power and TREP cells
cepip_example	Download the SEA-AD example data
cepip_example_clear	Delete the cached example data
cepip_fit	Fit the CEP-IP GAM
cepip_groups	Cell groups for downstream analyses
cepip_ip	Inflection point (IP) and IP reliability score (IPRS)
cepip_save	Save the tables and plots of one arm
cepip_screen	Spearman-Kendall dual-filter screen for partner genes
cepip_skcs	Spearman-Kendall cell-level scores (SKCS)
cepip_toy	Simulated example data
cepip_validate	Validate the CMRF Module by refitting the CEP-IP GAM (Validation1)
plot_associate	Forest plot of donor-level associations
plot_band	Plot the formation of the CMRF band (Figure 6)
plot_copula	Plot the cells and the CMRF band in copula space
plot_deg	Volcano plot of one differential expression contrast
plot_donor	Plot the per-donor Module Post-IP percentage
plot_fit	Plot the CEP-IP GAM with the inflection point
plot_module	Pitcher plot of the CMRF classes in copula space (Figure 8A)
plot_pitcher	Pitcher plot of the SKCS scores
plot_prss	Plot the PRSS search over the basis dimension k
plot_residual	Plot the residual GAM R(x) and the IP
plot_rskfcv	Plot the RSk-fCV gate of CMRF Stage 2 (Figure 7)
plot_screen	Plot the partner-gene screen of one GOI
plot_validate	Plot the Validation1 refit of the CMRF Module
print.cepip_figure	Draw a multi-panel cepip figure