data-raw/qpcr-data-names.r

In rnabioco/eda: Practical Biological Data Analysis in R/RStudio

library(tidyverse)

sample <- c('wt', 'mut')
gene <- c('IFN', 'ACTIN')
time <- c(0, 12, 24, 48)
rt <- c('+', '-') # reverse transcriptase added?
rep <- 1:3

set.seed(47681)
sample_data <- crossing(sample, time, gene, rep, rt)

plus_rts <- filter(sample_data, rt == "+")

t0 <- filter(plus_rts, time == 0) %>% rowwise() %>% mutate(exp = sample(5:15, 1))
t12 <- filter(plus_rts, time == 12) %>% rowwise() %>% mutate(exp = sample(45:55, 1))
t24 <- filter(plus_rts, time == 24) %>% rowwise() %>% mutate(exp = sample(95:100, 1))
t48 <- filter(plus_rts, time == 48) %>% rowwise() %>% mutate(exp = sample(350:600, 1))

plus_rts <- bind_rows(t0, t12, t24, t48)

# add multiplier for genes
ifns <- filter(plus_rts, gene == "IFN") %>% mutate(exp = exp * 1.5)
actins <- filter(plus_rts, gene == "ACTIN") %>% mutate(exp = exp * 0.2)
plus_rts <- bind_rows(ifns, actins)

minus_rts <- filter(sample_data, rt == "-") %>% mutate(exp = 0)

sample_data <- bind_rows(plus_rts, minus_rts) %>% arrange(sample, time, gene, rep)

qpcr_names <- sample_data %>%
  unite(name, sample, time, gene, rt, rep, sep = "_") %>%
  pluck("name") %>%
  matrix(nrow = 8, ncol = 12) %>%
  as_tibble() %>%
  set_names(nm = 1:12) %>%
  mutate(row = toupper(letters[1:8])) %>%
  select(row, everything())

qpcr_data <- sample_data %>%
  pluck("exp") %>%
  matrix(nrow = 8, ncol = 12) %>%
  as_tibble() %>%
  set_names(nm = 1:12) %>%
  mutate(row = toupper(letters[1:8])) %>%
  select(row, everything())

devtools::use_data(qpcr_names, compress = 'xz', overwrite = TRUE)
devtools::use_data(qpcr_data, compress = 'xz', overwrite = TRUE)