process_peak_area: Convert peak areas to concentration (nmol/g dry soil)

In mlfelice/plfaR: Interface for Analyzing IonVantage 13C-PLFA Data

Convert peak areas to concentration (nmol/g dry soil)

Description

This function takes a formatted peak list and carries out blank subtraction and calculates kval in order to convert peak area for each peak to concentration.

Usage

process_peak_area(
  dat,
  standard_fnames,
  mw_df = lipid_reference,
  standard_conc = 250,
  inj_vol = 2,
  standard = "13:0",
  soil_wt_df,
  vial_vol = 50,
  blanks
)

Arguments

dat	Dataframe or tibble with named PLFA peak data following format specified by import_batch().
standard_fnames	Character vector with names of samples to be used as standards for calculating the kval. Names should match names in DataFileName column of input dataframe.
mw_df	Dataframe including all lipids (fame column) of interest and their associated molecular weights (molecular_weight_g_per_mol column). By default, this function uses the included lipid_reference dataframe.
standard_conc	Numeric value indicating the concentraion of standard in ng/uL. Default is 250 ng/uL.
inj_vol	Volume of sample injected into GC in uL. Default is 2uL.
standard	String indicating the lipid used as the standard. Default is 13:0.
soil_wt_df	Dataframe or tibble containing the dry weight (g) of soil used for lipid extraction for each sample.
vial_vol	Volume solution run on GC. Default is 50 uL
blanks	Vector of the names of samples run as blanks. This should include all samples you want to use for peak subtraction (eg. 13:0 and 19:0) in most cases.

Value

Tibble similar to input with the addition of concentration column.

mlfelice/plfaR documentation built on June 9, 2022, 4:28 p.m.