pmartR (version 2.4.6)

as.nmrData: Create pmartR Object of Class nmrData

Description

Converts several data frames of NMR-generated metabolomic data to an object of the class 'nmrData'. Objects of the class 'nmrData' are lists with two obligatory components, e_data and f_data. An optional list component, e_meta, is used if analysis or visualization at other levels (e.g. metabolite identification) is also desired.

Usage

as.nmrData(
  e_data,
  f_data,
  e_meta = NULL,
  edata_cname,
  fdata_cname,
  emeta_cname = NULL,
  techrep_cname = NULL,
  ...
)

Value

Object of class nmrData

Arguments

e_data

a $p\times n+1$ data frame of expression data, where $p$ is the number of metabolites observed and $n$ is the number of samples. Each row corresponds to data for one metabolite. One column specifying a unique identifier for each metabolite (row) must be present.

f_data

a data frame with $n$ rows. Each row corresponds to a sample with one column giving the unique sample identifiers found in e_data column names and other columns providing qualitative and/or quantitative traits of each sample.

e_meta

an optional data frame with $p$ rows. Each row corresponds to a metabolite with one column giving metabolite names (must be named the same as the column in e_data) and other columns giving meta information.

edata_cname

character string specifying the name of the column containing the metabolite identifiers in e_data and e_meta (if applicable).

fdata_cname

character string specifying the name of the column containing the sample identifiers in f_data.

emeta_cname

character string specifying the name of the column containing the mapped identifiers in e_meta (if applicable). Defaults to NULL. Can be the same as edata_cname, if desired. If e_meta is NULL, then either do not specify emeta_cname or specify it as NULL.

techrep_cname

character string specifying the name of the column in f_data that specifies which samples are technical replicates. This column is used to collapse the data when combine_techreps is called on this object. Defaults to NULL (no technical replicates).

...

further arguments

Author

Lisa Bramer, Kelly Stratton

Details

Objects of class 'nmrData' contain some attributes that are referenced by downstream functions. These attributes can be changed from their default value by manual specification. A list of these attributes as well as their default values are as follows:

data_scale	Scale of the data provided in e_data. Acceptable values are 'log2', 'log10', 'log', and 'abundance', which indicate data is log base 2, base 10, natural log, or raw abundance, respectively. Default is 'abundance'.
is_normalized	A logical argument, specifying whether the data has been normalized or not. Default value is FALSE.
nmr_norm	A logical argument, specifying whether the data has been normalized either to a spiked in metabolite or to a property taking sample-specific values
#'
norm_info	Default value is an empty list, which will be populated with a single named element is_normalized = is_normalized. When a normalization is applied to the data, this becomes populated with a list containing the normalization function, normalization subset and subset parameters, the location and scale parameters used to normalize the data, and the location and scale parameters used to backtransform the data (if applicable).
data_types	Character string describing the type of data (e.g.'binned' or 'identified', for NMR data). Default value is NULL.

Computed values included in the data_info attribute are as follows:

num_edata	The number of unique edata_cname entries.
num_miss_obs	The number of missing observations.
num_emeta	The number of unique emeta_cname entries.
prop_missing	The proportion of e_data values that are NA.
num_samps	The number of samples that make up the columns of e_data.
meta_info	A logical argument, specifying where the e_meta is provided.

See Also

as.metabData

normalize_nmr

Examples

if (FALSE) { # requireNamespace("pmartRdata", quietly = TRUE)
library(pmartRdata)
mynmrData <- as.nmrData(
  e_data = nmr_identified_edata,
  f_data = nmr_identified_fdata,
  edata_cname = "Metabolite",
  fdata_cname = "SampleID",
  data_type = "identified"
)
}