## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>", fig.width = 7, fig.height = 5)
library(cepip)

## ----toy----------------------------------------------------------------------
d <- cepip_toy
d$y <- cepip_composite(d, paste0("P", 1:8))
res <- cepip(d$x, d$y, donor = d$donor, id = d$id, cmrf = TRUE, tests = FALSE)
res

## ----toy-plots, fig.height = 5------------------------------------------------
plot_fit(res)
plot_residual(res$ip)
plot_module(res$cmrf)

## ----band, fig.width = 12, fig.height = 9-------------------------------------
b <- cepip_band(res$skcs, res$ip, kappa = 0.5, bw = 0.1)
plot_band(b)

## ----gate, eval = FALSE-------------------------------------------------------
# cm <- cepip_cmrf(band = b, workers = 2)
# plot_rskfcv(cm, "first")
# plot_rskfcv(cm, "last")

## ----donor--------------------------------------------------------------------
dp <- cepip_donor(res)
head(dp)

## ----deg, eval = FALSE--------------------------------------------------------
# deg <- cepip_deg(res, expr, contrast = c("PostIP_vs_PreIP", "PostIP_vs_NMPost"))
# plot_deg(deg, "PostIP_vs_PreIP")

## ----assoc, eval = FALSE------------------------------------------------------
# tab <- merge(dp, donor_metadata, by = "donor")
# as <- cepip_associate(tab, "pct_PostIP", outcomes = c("MMSE", "Braak"),
#                       covariates = c("age", "sex", "PMI"))
# plot_associate(as)

## ----screen, eval = FALSE-----------------------------------------------------
# sc <- cepip_screen(expr, donor = donor)
# head(sc$ranking)
# plot_screen(sc)

## ----seaad, eval = FALSE------------------------------------------------------
# pv <- cepip_example("pvm3")
# MT8 <- c("MT-ATP6", "MT-CO2", "MT-ND3", "MT-ND4", "MT-CYB", "MT-ND1", "MT-ND2", "MT-CO1")
# d <- pv[pv$region_set == "NeoC", ]
# res <- cepip(d[["MT-CO3"]], cepip_composite(d, MT8), donor = d$donor, id = d$barcode,
#              cmrf = TRUE, ip_k = 10, y_spine = d$composite_part8, workers = 4)
# cepip_save(list(NeoC = res), "PVM_3")