data-raw/brauer-gene-exp.R

In IDPT7810/practical-data-analysis: Practical Biological Data Analysis in R/RStudio

library(tidyverse)
library(devtools)

url <- "http://varianceexplained.org/files/Brauer2008_DataSet1.tds"

nutrient_names <- c(G = "Glucose", L = "Leucine", P = "Phosphate",
                    S = "Sulfate", N = "Ammonia", U = "Uracil")

brauer_gene_exp <- read_delim(url, delim = "\t") %>%
  separate(NAME, c("name", "BP", "MF", "systematic_name", "number"), sep = "\\|\\|") %>%
  mutate_at(.funs = funs(trimws), .vars = vars(name:systematic_name)) %>%
  select(-number, -GID, -YORF, -GWEIGHT) %>%
  gather(sample, expression, G0.05:U0.3) %>%
  separate(sample, c("nutrient", "rate"), sep = 1, convert = TRUE) %>%
  mutate(nutrient = plyr::revalue(nutrient, nutrient_names)) %>%
  filter(!is.na(expression), systematic_name != "")

devtools::use_data(brauer_gene_exp, overwrite = TRUE, compress = "xz")