Converts several data frames of lipid data to an
object of the class 'lipidData'. Objects of the class 'lipidData' 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. lipid class) is also desired.
as.lipidData(
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 lipids observed and \(n\) is the number of samples. Each row corresponds to data for one lipid. One column specifying a unique identifier for each lipid (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 lipid with one column giving lipid names (must be named the same as
the column in e_data) and other columns giving biomolecule meta information.
character string specifying the name of the column
containing the lipid 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 mapped identifiers in e_meta (if applicable). Can be the same as edata_cname, if desired.
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 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 lipidData
Objects of class 'lipidData' 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 (e.g. 'Positive ion' or ‘Negative ion’ for lipid 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. |
library(pmartRdata)
mylipid <- as.lipidData(
e_data = lipid_neg_edata,
f_data = lipid_neg_fdata,
edata_cname = "Lipid",
fdata_cname = "SampleID"
)