inst/data-raw/process/PMID28742858_Thivolet-2017/process.R

In avucoh/nPOD: What the Package Does (One Line, Title Case)

library(rvest)
library(tidyr)
library(dplyr)

tab2 <- read_html("https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5526536/table/pone.0182027.t002/") %>% html_table()
tab2 <- tab2[[2]] %>%
  as_tibble() %>%
  rename(ID = `nPOD #`) %>%
  rename_at(2:6, function(x) gsub("-", "", x)) %>%
  filter(grepl("^6", ID)) %>% # remove group summary rows
  separate(IP3R2, c("IP3R2", "IP3R2_SEM"), "±") %>% # separate values and SEM values
  separate(TOM20, c("TOM20", "TOM20_SEM"), "±") %>%
  separate(MFN2, c("MFN2", "MFN2_SEM"), "±") %>%
  separate(VDAC1, c("VDAC1", "VDAC1_SEM"), "±") %>%
  separate(PLA, c("PLA", "PLA_SEM"), "±") %>%
  mutate_all(as.numeric)

# rename PLA to IP3R2.VDAC1 (IP3R2-VDAC1 interactions quantified by in situ proximity ligation assay (PLA))
# since that is clearer
tab2 <- tab2 %>%
  rename_all(function(x) gsub("PLA", "IP3R2.VDAC1", x))

write.table(tab2, file = "PMID28742858_1_Thivolet-2017.tsv", sep = "\t", row.names = F, quote = F)