normalize_istd: Normalize each class by its corresponding internal...

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

Normalize each class by its corresponding internal standard(s).

Description

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.

Usage

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

Arguments

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.

Value

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

Examples

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
)

ahmohamed/lipidr documentation built on July 7, 2023, 2:22 a.m.