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Normalize peak table or chromatograms

Source: R/attach_metadata.R
normalize_data.Rd

Normalizes peak table or list of chromatograms by specified column in sample metadata. Metadata must first be attached to peak_table using attach_metadata.

Usage

normalize_data(
  peak_table,
  column,
  chrom_list,
  what = c("peak_table", "chrom_list"),
  by = c("meta", "peak")
)

Arguments

peak_table

A `peak_table` object

column

The name of the column containing the weights.

chrom_list

List of chromatograms for normalization. The samples must be in same order as the peak_table. If no argument is provided here, the function will try to find the chrom_list object used to create the provided peak_table.

what

`peak_table` or list of chromatograms (`chrom_list`).

by

Whether to normalize by a column in sample metadata (meta) or by a column in the peak table itself (peak).

Value

A peak_table object where the peaks are normalized by the mass of each sample.

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