figure2.R

# --------------------------------------------------------------------------------- #
# Neighborhood-Level Deprivation and Survival in Lung Cancer
# --------------------------------------------------------------------------------- #
#
# Figure 2: Liquid biopsy epigenetic markers for lung cancer DNA methylation are 
# associated with lung cancer stage and NDI.
#
# Created by: Ian D. Buller, Ph.D., M.A. (@idblr)
# Created on: 2023-06-22
#
# Most recently modified by: @idblr
# Most recently modified on: 2024-08-06
#
# Notes:
# A) 2022-10-30 (@idblr): Initial script created by Ignacio Jusué-Torres, MD
# B) 2023-04-26 (@idblr): Updated script created by Ignacio Jusué-Torres, MD
# C) Note: values computed here were then imported into GraphPad Prism to generate 
#    the full figure
# D) 2024-07-10 (@idblr): Re-formatted code
# E) 2024-08-06 (@idblr): Re-formatted code
# --------------------------------------------------------------------------------- #

# ---------------- #
# DATA IMPORTATION #
# ---------------- #

source(file.path('code', 'preparation.R'))

# -------------------- #
# ADDITIONAL LIBRARIES #
# -------------------- #

loadedPackages <- c('stats')
suppressMessages(invisible(lapply(loadedPackages, library, character.only = TRUE)))

# -------- #
# FIGURE 2 #
# -------- #

# Figure 2A
cor.test(
  CANCER$STAGEnum,
  CANCER$HOXA7.Plasma,
  mu = 0,
  alt = 'two.sided',
  method = c('spearman'),
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
cor.test(
  CANCER$STAGEnum,
  CANCER$SOX17..Plasma,
  mu = 0,
  alt = 'two.sided',
  method = c('spearman'),
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
cor.test(
  CANCER$STAGEnum,
  CANCER$ZPF42..Plasma,
  mu = 0,
  alt = 'two.sided',
  method = c('spearman'),
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
cor.test(
  CANCER$STAGEnum,
  CANCER$TAC1.Plasma,
  mu = 0,
  alt = 'two.sided',
  method = c('spearman'),
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
cor.test(
  CANCER$STAGEnum,
  CANCER$HOXA9.Plasma,
  mu = 0,
  alt = 'two.sided',
  method = c('spearman'),
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
cor.test(
  CANCER$STAGEnum,
  CANCER$CDO1.Plasma,
  mu = 0,
  alt = 'two.sided',
  method = c('spearman'),
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)

## Figure 2B
summary(STAGE1$HOXA7.Plasma)
summary(STAGE2$HOXA7.Plasma)
summary(STAGE3$HOXA7.Plasma)
summary(STAGE4$HOXA7.Plasma)
summary(STAGElow$HOXA7.Plasma)
summary(STAGEhigh$HOXA7.Plasma)

wilcox.test(
  STAGE1$HOXA7.Plasma,
  STAGE2$HOXA7.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  STAGE1$HOXA7.Plasma,
  STAGE3$HOXA7.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  STAGE1$HOXA7.Plasma,
  STAGE4$HOXA7.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  STAGElow$HOXA7.Plasma,
  STAGEhigh$HOXA7.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)

## Figure 2C
summary(STAGE1$SOX17..Plasma)
summary(STAGE2$SOX17..Plasma)
summary(STAGE3$SOX17..Plasma)
summary(STAGE4$SOX17..Plasma)
summary(STAGElow$SOX17..Plasma)
summary(STAGEhigh$SOX17..Plasma)

wilcox.test(
  STAGE1$SOX17..Plasma,
  STAGE2$SOX17..Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  STAGE1$SOX17..Plasma,
  STAGE3$SOX17..Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  STAGE1$SOX17..Plasma,
  STAGE4$SOX17..Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  STAGElow$SOX17..Plasma,
  STAGEhigh$SOX17..Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)

## Figure 2D
summary(STAGE1$ZPF42..Plasma)
summary(STAGE2$ZPF42..Plasma)
summary(STAGE3$ZPF42..Plasma)
summary(STAGE4$ZPF42..Plasma)
summary(STAGElow$ZPF42..Plasma)
summary(STAGEhigh$ZPF42..Plasma)

wilcox.test(
  STAGE1$ZPF42..Plasma,
  STAGE2$ZPF42..Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  STAGE1$ZPF42..Plasma,
  STAGE3$ZPF42..Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  STAGE1$ZPF42..Plasma,
  STAGE4$ZPF42..Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  STAGElow$ZPF42..Plasma,
  STAGEhigh$ZPF42..Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)

## Figure 2E
summary(STAGE1$TAC1.Plasma)
summary(STAGE2$TAC1.Plasma)
summary(STAGE3$TAC1.Plasma)
summary(STAGE4$TAC1.Plasma)
summary(STAGElow$TAC1.Plasma)
summary(STAGEhigh$TAC1.Plasma)

wilcox.test(
  STAGE1$TAC1.Plasma,
  STAGE1$TAC1.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  STAGE1$TAC1.Plasma,
  STAGE2$TAC1.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  STAGE1$TAC1.Plasma,
  STAGE4$TAC1.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  STAGElow$TAC1.Plasma,
  STAGEhigh$TAC1.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)

## Figure 2F
summary(STAGE1$HOXA9.Plasma)
summary(STAGE2$HOXA9.Plasma)
summary(STAGE3$HOXA9.Plasma)
summary(STAGE4$HOXA9.Plasma)
summary(STAGElow$HOXA9.Plasma)
summary(STAGEhigh$HOXA9.Plasma)

wilcox.test(
  STAGE1$HOXA9.Plasma,
  STAGE2$HOXA9.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  STAGE1$HOXA9.Plasma,
  STAGE3$HOXA9.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  STAGE1$HOXA9.Plasma,
  STAGE4$HOXA9.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  STAGElow$HOXA9.Plasma,
  STAGEhigh$HOXA9.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)

## Figure 2G
summary(STAGE1$CDO1.Plasma)
summary(STAGE2$CDO1.Plasma)
summary(STAGE3$CDO1.Plasma)
summary(STAGE4$CDO1.Plasma)
summary(STAGElow$CDO1.Plasma)
summary(STAGEhigh$CDO1.Plasma)

wilcox.test(
  STAGE1$CDO1.Plasma,
  STAGE1$CDO1.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  STAGE1$CDO1.Plasma,
  STAGE2$CDO1.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  STAGE1$CDO1.Plasma,
  STAGE3$CDO1.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  STAGElow$CDO1.Plasma,
  STAGEhigh$CDO1.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)

# Figure 2H
cor.test(
  CANCER$NDImesser_tr,
  CANCER$HOXA7.Plasma,
  mu = 0,
  alt = 'two.sided',
  method = c('spearman'),
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
cor.test(
  CANCER$NDImesser_tr,
  CANCER$TAC1.Plasma,
  mu = 0,
  alt = 'two.sided',
  method = c('spearman'),
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
cor.test(
  CANCER$NDImesser_tr,
  CANCER$CDO1.Plasma,
  mu = 0,
  alt = 'two.sided',
  method = c('spearman'),
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
cor.test(
  CANCER$NDImesser_tr,
  CANCER$SOX17..Plasma,
  mu = 0,
  alt = 'two.sided',
  method = c('spearman'),
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
cor.test(
  CANCER$NDImesser_tr,
  CANCER$ZPF42..Plasma,
  mu = 0,
  alt = 'two.sided',
  method = c('spearman'),
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
cor.test(
  CANCER$NDImesser_tr,
  CANCER$HOXA9.Plasma,
  mu = 0,
  alt = 'two.sided',
  method = c('spearman'),
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)

# Figure 2I
summary(NDI1$HOXA7.Plasma)
summary(NDI2$HOXA7.Plasma)
summary(NDI3$HOXA7.Plasma)
summary(NDI4$HOXA7.Plasma)
summary(LOWNDI$HOXA7.Plasma)
summary(HIGHNDI$HOXA7.Plasma)

wilcox.test(
  NDI1$HOXA7.Plasma,
  NDI2$HOXA7.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  NDI1$HOXA7.Plasma,
  NDI2 = 3$HOXA7.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  NDI1$HOXA7.Plasma,
  NDI4$HOXA7.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  LOWNDI$HOXA7.Plasma,
  HIGHNDI$HOXA7.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)

# Figure 2J
summary(NDI1$TAC1.Plasma)
summary(NDI2$TAC1.Plasma)
summary(NDI3$TAC1.Plasma)
summary(NDI4$TAC1.Plasma)
summary(LOWNDI$TAC1.Plasma)
summary(HIGHNDI$TAC1.Plasma)

wilcox.test(
  NDI1$TAC1.Plasma,
  NDI2$TAC1.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  NDI1$TAC1.Plasma,
  NDI2 = 3$TAC1.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  NDI1$TAC1.Plasma,
  NDI4$TAC1.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  LOWNDI$TAC1.Plasma,
  HIGHNDI$TAC1.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)

# Figure 2K
summary(NDI1$CDO1.Plasma)
summary(NDI2$CDO1.Plasma)
summary(NDI3$CDO1.Plasma)
summary(NDI4$CDO1.Plasma)
summary(LOWNDI$CDO1.Plasma)
summary(HIGHNDI$CDO1.Plasma)

wilcox.test(
  NDI1$CDO1.Plasma,
  NDI2$CDO1.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  NDI1$CDO1.Plasma,
  NDI2 = 3$CDO1.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  NDI1$CDO1.Plasma,
  NDI4$CDO1.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  LOWNDI$CDO1.Plasma,
  HIGHNDI$CDO1.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)

# Figure 2L
summary(NDI1$SOX17..Plasma)
summary(NDI2$SOX17..Plasma)
summary(NDI3$SOX17..Plasma)
summary(NDI4$SOX17..Plasma)
summary(LOWNDI$SOX17..Plasma)
summary(HIGHNDI$SOX17..Plasma)

wilcox.test(
  NDI1$SOX17..Plasma,
  NDI2$SOX17..Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  NDI1$SOX17..Plasma,
  NDI2 = 3$SOX17..Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  NDI1$SOX17..Plasma,
  NDI4$SOX17..Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  LOWNDI$SOX17..Plasma,
  HIGHNDI$SOX17..Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)

# Figure 2M
summary(NDI1$ZPF42..Plasma)
summary(NDI2$ZPF42..Plasma)
summary(NDI3$ZPF42..Plasma)
summary(NDI4$ZPF42..Plasma)
summary(LOWNDI$ZPF42..Plasma)
summary(HIGHNDI$ZPF42..Plasma)

wilcox.test(
  NDI1$ZPF42..Plasma,
  NDI2$ZPF42..Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  NDI1$ZPF42..Plasma,
  NDI2 = 3$ZPF42..Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  NDI1$ZPF42..Plasma,
  NDI4$ZPF42..Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  LOWNDI$ZPF42..Plasma,
  HIGHNDI$ZPF42..Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)

# Figure 2N
summary(NDI1$HOXA9.Plasma)
summary(NDI2$HOXA9.Plasma)
summary(NDI3$HOXA9.Plasma)
summary(NDI4$HOXA9.Plasma)
summary(LOWNDI$HOXA9.Plasma)
summary(HIGHNDI$HOXA9.Plasma)

wilcox.test(
  NDI1$HOXA9.Plasma,
  NDI2$HOXA9.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  NDI1$HOXA9.Plasma,
  NDI2 = 3$HOXA9.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  NDI1$HOXA9.Plasma,
  NDI4$HOXA9.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)
wilcox.test(
  LOWNDI$HOXA9.Plasma,
  HIGHNDI$HOXA9.Plasma,
  mu = 0,
  alt = 'two.sided',
  paired = FALSE,
  conf.int = TRUE,
  conf.level = 0.95,
  exact = FALSE
)

# ---------------------------------- END OF CODE ---------------------------------- #