normalize_nmr: Normalize an Object of Class nmrData

In pmartR/pmartRqc: Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data

Normalize an Object of Class nmrData

Description

The data is normalized either to a spiked-in metabolite or to a sample-specific property

Usage

normalize_nmr(
  omicsData,
  apply_norm = FALSE,
  backtransform = FALSE,
  metabolite_name = NULL,
  sample_property_cname = NULL
)

Arguments

omicsData	an object of the class 'nmrData'
apply_norm	logical, indicates whether normalization should be applied to omicsData$e_data. Defaults to FALSE. If TRUE, the normalization is applied to the data and an S3 object of the same class as omicsData (e.g. 'nmrData') with normalized values in e_data is returned. If FALSE, the normalization is not applied and an S3 object of the class nmrnormRes is returned, allowing some exploratory data analysis prior to subsequently applying the normalization.
backtransform	logical argument indicating if parameters for back transforming the data, after normalization, should be calculated. Defaults to FALSE. If TRUE, the parameters for back transforming the data after normalization will be calculated, and subsequently included in the data normalization if apply_norm is TRUE. See details for an explanation of how these factors are calculated.
metabolite_name	optional character string specifying the name of the (spiked in) metabolite in e_data to use for instrument normalization of the nmrData object. These values will be used to divide the raw abundance of the corresponding sample in e_data (if e_data is log transformed, this function accounts for that and returns normalized data on the same scale it was provided). If using this argument, the 'sample_property_cname' argument should not be specified.
sample_property_cname	optional character string specifying the name of the column in f_data containing information to use for instrument normalization of the nmrData object, such as a concentration. These values will be used to divide the raw abundance of the corresponding sample in e_data (if e_data is log transformed, this function accounts for that by temporarily un-log transforming the data and then returning normalized data on the same scale it was provided). If using this argument, the 'metabolite_name' argument should not be specified.

Details

There are two ways to specify the information needed for performing instrument normalization on an nmrData object:

1. specify metabolite_name. This should be used when normalization to a spiked in standard is desired. Here metabolite_name gives the name of the metabolite in e_data (and e_meta, if present) corresponding to the spiked in standard. If any samples have a missing value for this metabolite, an error is returned.

2. specify sample_property_cname. This should be used when normalizing to a sample property, such as concentration, is desired. Here, sample_property_cname gives the name of the column in f_data which contains the property to use for normalization. If any samples have a missing value for this column, and error is returned.

Value

If apply_norm is TRUE, an object of class 'nmrData', normalized and with information about the normalization process in 'nmr_info'. Otherwise, an object of class 'nmrnormRes' is returned, with the same info about normalization in attribute 'nmr_info' to be passed to plotting and summary functions.

Backtransform

The purpose of back transforming data is to ensure values are on a scale similar to their raw values before normalization. The following values are calculated and/or applied for backtransformation purposes:

If normalization using a metabolite in e_data is specified	location parameter is the median of the values for metabolite_name
If normalization using a sample property in f_data is specified	location parameter is the median of the values in sample_property

See examples below.

Examples

library(pmartRdata)

# Normalize using a metabolite (this is merely an example of how to use this specification;
# the metabolite used was not actually spiked-in for the purpose of normalization)
mynmr <- edata_transform(
  omicsData = nmr_identified_object,
  data_scale = "log2"
)
nmr_norm <- normalize_nmr(
  omicsData = mynmr, apply_norm = TRUE,
  metabolite_name = "unkm1.53",
  backtransform = TRUE
)

# Normalization using a sample property
mynmr <- edata_transform(
  omicsData = nmr_identified_object,
  data_scale = "log2"
)
nmr_norm <- normalize_nmr(
  omicsData = mynmr, apply_norm = TRUE,
  sample_property_cname = "Concentration",
  backtransform = TRUE
)

pmartR/pmartRqc documentation built on April 25, 2024, 6:18 a.m.