data-raw/data_normalized.R

In ahmohamed/lipidr: Data Mining and Analysis of Lipidomics Datasets

# Internal script to update the dataset, in case of future changes.
# Should be called once before each package release.
library(lipidr)
datadir <- system.file("extdata", package = "lipidr")
filelist <- list.files(datadir, "data.csv", full.names = TRUE)
d <- read_skyline(filelist)
clinical_file <- system.file("extdata", "clin.csv", package = "lipidr")
d <- add_sample_annotation(d, clinical_file)
d_summarized <- summarize_transitions(d, method = "average")
data_normalized <- normalize_pqn(d_summarized, measure = "Area", exclude = "blank", log = TRUE)

usethis::use_data(data_normalized, overwrite = TRUE)