Selection of post-treatment liquid biopsy timepoint for molecular analyses
Last updated: 2025-03-27
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Time distribution of each blood draw in CheckPAC and PACTO studies.
library(data.table)
library(here)
library(lubridate)
library(readxl)
library(tidyverse)supplementary_checkpac <- read_excel(here("data/supplementary_tables.xlsx"),
sheet = "Table S2", range = "A2:M219")
supplementary_pacto <- read_excel(here("data/supplementary_tables.xlsx"),
sheet = "Table S5", range = "A2:L207")# Keep first four visits for CheckPAC
dates_checkpac <- supplementary_checkpac %>%
mutate(Visit = str_extract(Sample, "(?<=CGPLPA[0-9]{1,10}P)[\b0-9]{1,2}")) %>%
mutate(Visit = as.numeric(Visit)) %>%
replace_na(list(Visit = 0)) %>%
filter(Visit %in% c(0:3)) %>%
mutate(tp = case_when(Visit == 0 ~ "Baseline",
Visit == 1 ~ "Cycle 1",
Visit == 2 ~ "Endpoint",
Visit == 3 ~ "Follow-up"))
# Print median days from treatment
dates_checkpac %>%
group_by(tp) %>%
summarize(`Days from Tx init` = median(`Days from Treatment Initiation`))# A tibble: 4 × 2
tp `Days from Tx init`
<chr> <dbl>
1 Baseline -1.5
2 Cycle 1 13
3 Endpoint 55
4 Follow-up 97 # Keep first four visit for PACTO
dates_pacto <- supplementary_pacto %>%
mutate(Visit = str_extract(Sample, "(?<=CGPLPA[0-9]{1,10}P)[\b0-9]{1,2}")) %>%
mutate(Visit = as.numeric(Visit)) %>%
replace_na(list(Visit = 0)) %>%
filter(Visit %in% c(0:3)) %>%
mutate(tp = case_when(Visit == 0 ~ "Baseline",
Visit == 1 ~ "Cycle 1",
Visit == 2 ~ "Endpoint",
Visit == 3 ~ "Follow-up"))
# Print median days from treatment
dates_pacto %>%
group_by(tp) %>%
summarize(`Days from Tx init` = median(`Days from Treatment Initiation`))# A tibble: 4 × 2
tp `Days from Tx init`
<chr> <dbl>
1 Baseline 0
2 Cycle 1 29
3 Endpoint 58
4 Follow-up 116.# Combine data
checkpac_dates_full <- dates_checkpac %>%
mutate(Trial = "CHECKPAC") %>%
select(Sample, `Days from Treatment Initiation`, tp, Trial)
pacto_dates_full <- dates_pacto %>%
mutate(Trial = "PACTO") %>%
select(Sample, `Days from Treatment Initiation`, tp, Trial)
alldates_pacto_checkpac <- bind_rows(pacto_dates_full,
checkpac_dates_full)ggplot(alldates_pacto_checkpac,
aes(tp, `Days from Treatment Initiation`, fill = Trial)) +
geom_boxplot() +
ylab("Days from baseline") + xlab("Draws") +
theme_classic()
sessionInfo()R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS 15.3.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 purrr_1.0.4
[5] readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 ggplot2_3.5.1
[9] tidyverse_2.0.0 readxl_1.4.5 lubridate_1.9.4 here_1.0.1
[13] data.table_1.17.0 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] utf8_1.2.4 sass_0.4.9 generics_0.1.3 stringi_1.8.4
[5] rematch_2.0.0 hms_1.1.3 digest_0.6.37 magrittr_2.0.3
[9] evaluate_1.0.3 grid_4.4.1 timechange_0.3.0 fastmap_1.2.0
[13] cellranger_1.1.0 rprojroot_2.0.4 jsonlite_1.9.1 processx_3.8.6
[17] whisker_0.4.1 ps_1.9.0 promises_1.3.2 httr_1.4.7
[21] scales_1.3.0 jquerylib_0.1.4 cli_3.6.4 rlang_1.1.5
[25] munsell_0.5.1 withr_3.0.2 cachem_1.1.0 yaml_2.3.10
[29] tools_4.4.1 tzdb_0.4.0 colorspace_2.1-1 httpuv_1.6.15
[33] vctrs_0.6.5 R6_2.6.1 lifecycle_1.0.4 git2r_0.35.0
[37] fs_1.6.5 pkgconfig_2.0.3 callr_3.7.6 pillar_1.10.1
[41] bslib_0.9.0 later_1.4.1 gtable_0.3.6 glue_1.8.0
[45] Rcpp_1.0.14 xfun_0.51 tidyselect_1.2.1 rstudioapi_0.17.1
[49] knitr_1.49 farver_2.1.2 htmltools_0.5.8.1 labeling_0.4.3
[53] rmarkdown_2.29 compiler_4.4.1 getPass_0.2-4