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Target factory for PCA run and missing values imputation on each omics dataset

Source: R/multidataset_pca.R
pca_complete_data_factory.Rd

Creates a list of targets that perform a PCA run for each omics dataset from a MultiDataSet object using dynamic branching, and imputes the missing values in those datasets using the results of the PCA runs.

Usage

pca_complete_data_factory(
  mo_data_target,
  dataset_names = NULL,
  target_name_prefix = "",
  complete_data_name = NULL,
  ...
)

Arguments

mo_data_target

Symbol, the name of the target containing the MultiDataSet object.

dataset_names

Character vector, the names of the datasets on which a PCA should be run. If NULL, a PCA will be run on all datasets. Default value is NULL.

target_name_prefix

Character, prefix to add to the name of the targets created by the factory. Default value is "".

complete_data_name

Character, the name of the target containing the MultiDataSet with missing data imputed to be created. If NULL, will be selected automatically. Default value is NULL.

...

Further arguments passed to the run_pca_matrix() function.

Value

A List of targets. If target_name_prefix = "" and complete_data_name = NULL, the following targets are created:

  • dataset_names_pca: target containing a character vector that gives the names of the datasets on which a PCA should be run.

  • dataset_mats_pca: a dynamic branching target that applies the get_dataset_matrix() function to each dataset specified in dataset_names. The results are saved in a list. Note that because it is using dynamic branching, the names of the list are not meaningful. Rather, use sapply(pca_pca_runs_listruns_list, attr, "dataset_name") to assess which element of the list corresponds to which omics dataset.

  • pca_runs_list: a dynamic branching target that applies the run_pca_matrix() function to each matrix in dataset_mats_pca. The results are saved in a list. Note that because it is using dynamic branching, the names of the list are not meaningful. Rather, use sapply(pca_runs_list, attr, "dataset_name") to assess which element of the list corresponds to which omics dataset.

  • complete_set: a target that returns a MultiDataSet in which missing values have been imputed.

Examples

if (FALSE) { # \dontrun{
## in the _targets.R
library(moiraine)
list(
  # ... code for importing datasets etc

  ## mo_set is the target containing the MultiDataSet object
  ## Example 1: running a PCA on all datasets
  run_pca_factory(mo_set),

  ## Example 2: running a PCA on 'rnaseq' and 'metabolome' datasets
  run_pca_factory(
    mo_set,
    c("rnaseq", "metabolome"),
    complete_data_name = "mo_data_complete"
  )
)
} # }