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Normalize peak table or chromatograms

Source: R/normalize_data.R
normalize_data.Rd

Normalizes peak table or list of chromatograms by a column in the sample metadata or in the peak table. For normalization by sample metadata, the metadata must first be attached to the peak_table using attach_metadata.

Usage

normalize_data(
  peak_table,
  column,
  chrom_list = NULL,
  what = c("peak_table", "chrom_list"),
  by = NULL,
  on_invalid = c("warn", "error", "silent")
)

Arguments

peak_table

A peak_table object.

column

The name of the column to be used for normalization.

chrom_list

List of chromatograms for normalization. The samples must be in same order as the peak_table. If omitted, the function will attempt to find it automatically using the pointer from the peak_table.

what

Output type to return: either "peak_table" (default) or "chrom_list".

by

Whether to normalize by a column in sample metadata (meta) or by a column in the peak table (peak). By default, this parameter is inferred based on the column name.

on_invalid

How to handle invalid normalization values (i.e. zero, negative, or NA values). One of "warn" (the default), "silent", or "error". Invalid values are replaced with NA unless "error" is chosen.

Value

Either a normalized peak_table object or a normalized chrom_list, depending on the value of what.

See also

get_peaktable attach_metadata

Author

Ethan Bass

Examples

data(pk_tab)
path <- system.file("extdata", "Sa_metadata.csv", package = "chromatographR")
meta <- read.csv(path)

# normalize by sample mass
pk_tab <- attach_metadata(peak_table = pk_tab, metadata = meta, column="vial")
norm <- normalize_data(pk_tab, "mass", what = "peak_table")

# normalize by internal standard
norm <- normalize_data(pk_tab, column = "V16", by = "peak")