norm_peaks {GCalignR}

Normalisation of peak abundancies

Description

Calculates the relative abundance of a peak by normalising an intensity measure with regard to the cumulative abundance of all peaks that are present within an individual sample. The desired measure of peak abundance needs to be included in a column of the input dataset aligned with align_chromatograms.

Usage

norm_peaks(
  data,
  conc_col_name = NULL,
  rt_col_name = NULL,
  out = c("data.frame", "list")
)

Arguments

data

Object of class GCalign created with align_chromatograms or a list of data frames that contain peak list of individual samples.

conc_col_name

Character giving the name of a column in data containing a variable describing the abundance of peaks (e.g. peak area or peak height).

rt_col_name

A character giving the name of the column containing the retention times. The decimal separator needs to be a point.

out

character defining the format of the returned data. Either "List" or "data.frame".

Value

Depending on out either a list of data frame or a single data frame were rows represent samples and columns relative peak abundances. Abundances are given as percentages.

@author Martin Stoffel ([e-mail]) & Meinolf Ottensmann ([e-mail])

Examples

## aligned gc-dataset
data("aligned_peak_data")
## returns normalised peak area
norm_peaks(data = aligned_peak_data, conc_col_name = "area", rt_col_name = "time")