normalize_istd: Normalize each class by its corresponding internal...
In lipidr: Data Mining and Analysis of Lipidomics Datasets

Description Usage Arguments Value Examples

Normalize each class by its corresponding internal standard(s). Lipid classes are normalized using corresponding internal standard(s) of the same lipid class. If no corresponding internal standard is found the average of all measured internal standards is used instead.

1	normalize_istd(data, measure = "Area", exclude = "blank", log = TRUE)

`data`	LipidomicsExperiment object.
`measure`	Which measure to use as intensity, usually Area, Area Normalized or Height. Default is `Area`.
`exclude`	Samples to exclude, can be either: "blank" - automatically detected blank samples and exclude them logical vector with the same length as samples. Default.
`log`	whether the normalized values should be log2 transformed. Default is `TRUE`.

A LipidomicsExperiment object with normalized values. Each molecule is normalized against the internal standard from the same class.

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")

# Normalize data that have been summarized (single value per molecule).
data_norm_istd <- normalize_istd(
  d_summarized,
  measure = "Area", exclude = "blank", log = TRUE
)