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7-compare_summarized_lists.R
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7-compare_summarized_lists.R
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# This scripts creates a list of all pairwise comparisons between covidc, covidm,
# the a549-sars2 and the ace2 consensus drug lists.
library(tidyverse)
mark_nonfda <- function(df) {
out <- df %>%
mutate(
fda_status = case_when(
str_detect(compound, "CHEMBL") ~ "non_fda",
str_detect(compound, "SCHEMBL") ~ "non_fda",
str_detect(compound, "^\\d+") ~ "non_fda",
str_detect(compound, "^[A-Z]\\d*\\w*\\-?\\s?\\d+") ~ "non_fda",
str_detect(compound, "[Ii]nhibitor") ~ "non_fda",
str_detect(compound, "^Broad") ~ "non_fda",
str_detect(compound, "^BRD*") ~ "non_fda",
str_detect(compound, "^UNII") ~ "non_fda",
str_detect(compound, "omer") ~ "non_fda",
str_detect(compound, "^Tyrphostin") ~ "non_fda",
TRUE ~ "fda"
)
)
out
}
top_drugs <-
c(
"Gemcitabine",
"Trametinib",
"Withaferin A",
"Saracatinib",
"Erlotinib",
"Alvocidib",
"Itrazole",
"Elesclomol",
"Dasatinib",
"Panobinostat",
"Gallocatechin Gallate",
"Genistein",
"Imatinib",
"Dexamethasone Acetate",
"Simvastatin",
"Sirolimus",
"Tamoxifen"
)
covidc <- read_csv("results/covidc-summarized-dataset.csv") %>%
select(compound, avg, sdev) %>%
mark_nonfda() %>%
mutate(covidc = 2 ^ 0)
covidm <- read_csv("results/covidm-summarized-dataset.csv") %>%
select(compound, avg, sdev) %>%
mark_nonfda() %>%
mutate(covidm = 2 ^ 1)
a549 <- read_csv("results/sars2-summarized-dataset.csv") %>%
select(compound, avg, sdev) %>%
mark_nonfda() %>%
mutate(a549 = 2 ^ 2)
ace2 <- read_csv("results/ace2-summarized-dataset.csv") %>%
select(compound, avg, sdev) %>%
mark_nonfda() %>%
mutate(ace2 = 2 ^ 3)
selected_list <- read_csv("results/sars2-summarized-dataset.csv") %>%
select(compound, avg, sdev) %>%
mark_nonfda() %>%
filter(avg > 0.5, sdev < 0.06, fda_status == "fda") %>%
mutate(selected = 2 ^ 4,
top = if_else(compound %in% top_drugs, 2 ^ 5, 0))
all_drugs <- covidc %>%
full_join(covidm, by = c("compound", "avg", "sdev", "fda_status")) %>%
full_join(a549, by = c("compound", "avg", "sdev", "fda_status")) %>%
full_join(ace2, by = c("compound", "avg", "sdev", "fda_status")) %>%
full_join(selected_list, by = c("compound", "avg", "sdev", "fda_status")) %>%
mutate(covidc = if_else(is.na(covidc), 0, covidc),
covidm = if_else(is.na(covidm), 0, covidm),
a549 = if_else(is.na(a549), 0, a549),
ace2 = if_else(is.na(ace2), 0, ace2),
selected = if_else(is.na(selected), 0, selected),
top = if_else(is.na(top), 0, top),
ident = covidc + covidm + a549 + ace2 + selected + top) %>%
write_csv("results/all_drugs_combinations_comparison.csv")