Converts several data frames of RNA-seq transcript data to
an object of the class 'seqData'. Objects of the class 'seqData' 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, protein, pathway) is also desired.
as.seqData(
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 RNA transcripts observed and \(n\) is the number of samples (an additional transcript identifier/name column should also be present somewhere in the data frame). Each row corresponds to data for one transcript. One column specifying a unique identifier for each transcript (row) must be present. All counts are required to be raw for processing.
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. For library size normalization, this can be provided as part of f_data or calculated from columns in e_data.
an optional data frame with at least \(p\) rows. Each row
corresponds to a transcript with one column giving transcript names (must be
named the same as the column in e_data) and other columns giving biomolecule
meta information (e.g. mappings of transcripts to genes or proteins). Can be the same as edata_cname, if desired.
character string specifying the name of the column
containing the transcript 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. 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 seqData
Objects of class 'seqData' 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. Only 'counts' is valid for
'seqData'. |
| 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. |
| 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_zero_obs | The number of zero-value 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)
myseq <- as.seqData(
e_data = rnaseq_edata,
e_meta = rnaseq_emeta,
f_data = rnaseq_fdata,
edata_cname = "Transcript",
fdata_cname = "SampleName",
emeta_cname = "Transcript"
)