Converts several data frames of protein data to an
object of the class 'proData'. Objects of the class 'proData' 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. gene) is also desired.
as.proData(
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 proteins observed and \(n\) is the number of samples. Each row corresponds to data for one protein. One column specifying a unique identifier for each protein (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 \(p\) rows. Each row corresponds
to a protein with one column giving protein names (must be named the same
as the column in e_data) and other columns giving biomolecule meta information
(e.g. mappings of proteins to genes).
character string specifying the name of the column
containing the protein 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 gene 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 proData
Objects of class 'proData' 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
values 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)
myproData <- as.proData(
e_data = pro_edata,
f_data = pro_fdata,
edata_cname = "RazorProtein",
fdata_cname = "SampleID",
is_normalized = TRUE
)