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.
as.isobaricpepData(
e_data,
f_data,
e_meta = NULL,
edata_cname,
fdata_cname,
emeta_cname = NULL,
techrep_cname = NULL,
...
)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.
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.
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).
character string specifying the name of the column
containing the peptide identifiers in e_data and e_meta (if
applicable).
character string specifying the name of the column
containing the sample identifiers in f_data.
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.
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
Object of class isobaricpepData and pepData.
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. |
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"
)