Converts several data frames of (unlabeled or global, as opposed to labeled) peptide data to an
object of the class 'pepData'. Objects of the class 'pepData' 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.pepData(
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 somewhere 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. 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.
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
Object of class pepData
Objects of class 'pepData' 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. |
| 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_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 whether e_meta is provided. |
library(pmartRdata)
mypepData <- as.pepData(
e_data = pep_edata,
e_meta = pep_emeta,
f_data = pep_fdata,
edata_cname = "Peptide",
fdata_cname = "SampleID",
emeta_cname = "RazorProtein"
)