as.isobaricpepData: Create pmartR Object of Class isobaricpepData

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

Create pmartR Object of Class isobaricpepData

Description

Converts several data frames of isobaric peptide data to an object of the class 'isobaricpepData'. Objects of the class 'isobaricpepData' 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. protein) is also desired.

Usage

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

Arguments

e_data	a p \times n + 1 data frame of expression data, where p is the number of peptides observed and n is the number of samples (an additional peptide identifier/name column should also be present in the data frame). Each row corresponds to data for one peptide. One column specifying a unique identifier for each peptide (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 at least p rows. Each row corresponds to a peptide with one column giving peptide names (must be named the same as the column in e_data) and other columns giving biomolecule meta information (e.g. mappings of peptides to proteins).
edata_cname	character string specifying the name of the column containing the peptide 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 protein identifiers (or other mapping variable) in e_meta (if applicable). Defaults to NULL. 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 containing the identifiers for the biological samples if the observations represent 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

Details

The class 'isobaricpepData' is meant to deal with labeled peptide data generated on instruments (e.g. TMT, iTRAQ) where a reference pool sample will be utilized for normalization.

If your data has already undergone normalization to the reference pool, you should specify isobaric_norm = T.

Objects of class 'isobaricpepData' 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 transformed, and raw abundance, respectively. Default is 'abundance'.
is_normalized	A logical argument, specifying whether the data has been normalized or not (this normalization refers to a statistical normalization, such as median centering or other methods). Default value is FALSE.
isobaric_norm	A logical argument, specifying whether the data has been normalized to the appropriate reference pool sample or not. Default value is FALSE
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, most commonly used for lipidomic data (lipidData objects) or NMR data (nmrData objects) but available for other data classes as well. 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_zero_obs	For seqData only: The number of zero observations.
num_emeta	The number of unique emeta_cname entries.
prop_missing	The proportion of e_data values that are NA.
prop_zeros	For seqData only: the proportion of zero counts observed in e_data values.
num_samps	The number of samples that make up the columns of e_data.
meta_info	A logical argument, specifying whether e_meta is provided.

Value

Object of class isobaricpepData and pepData.

Author(s)

Lisa Bramer

See Also

as.pepData

normalize_isobaric

Examples

library(pmartRdata)
mypep <- as.isobaricpepData(
  e_data = isobaric_edata,
  e_meta = isobaric_emeta,
  f_data = isobaric_fdata,
  edata_cname = "Peptide",
  fdata_cname = "SampleID",
  emeta_cname = "Protein"
)

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