Target factory for feature preselection based on sPLS-DA

Creates a list of targets to perform feature preselection on datasets from a MultiDataSet object with sPLS-DA (from the mixOmics package).

Usage

feature_preselection_splsda_factory(
  mo_data_target,
  group,
  to_keep_ns,
  to_keep_props = NULL,
  target_name_prefix = "",
  filtered_set_target_name = NULL,
  multilevel = NULL,
  seed_perf = NULL,
  seed_run = NULL,
  ...
)

Arguments

mo_data_target

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

group

Character, the column name in the samples information data-frame to use as samples group.

to_keep_ns

Named integer vector, the number of feature to retain in each dataset to be prefiltered (names should correspond to a dataset name). Value should be less than the number of features in the corresponding dataset. Set to NULL in order to use to_keep_props instead.

to_keep_props

Named numeric vector, the proportion of features to retain in each dataset to be prefiltered (names should correspond to a dataset name). Value should be > 0 and < 1. Will be ignored if to_keep_ns is not NULL.

target_name_prefix

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

filtered_set_target_name

Character, the name of the final target containing the filtered MultiDataSet object. If NULL, a name will automatically be supplied. Default value is NULL.

multilevel

Character vector of length 1 or 3 to be used as information about repeated measurements. See get_input_splsda() for details. Default value is NULL (no repeated measurements).

seed_perf

Named integer vector, the seed to use for the perf_splsda() function for each dataset. The length and names should match those of to_keep_ns or to_keep_props. If not named, the values will be used in order of the datasets in to_keep_ns or to_keep_props. Default value is NULL, i.e. no seed is set.

seed_run

Named integer vector, the seed to use for the run_splsda() function for each dataset. The length and names should match those of to_keep_ns or to_keep_props. If not named, the values will be used in order of the datasets in to_keep_ns or to_keep_props. Default value is NULL, i.e. no seed is set.

...

Further arguments passed to the perf_splsda function.

Value

A list of target objects. With target_name_prefix = "" and filtered_set_target_name = NULL, the following targets are created:

• splsda_spec: generates a grouped tibble where each row corresponds to one dataset to be filtered, with the columns specifying each dataset name, and associated values from to_keep_ns and to_keep_props.

  • individual_splsda_input: a dynamic branching target that runs the get_input_splsda() function for each dataset.

• individual_splsda_perf: a dynamic branching target that runs the perf_splsda() function for each dataset.

• individual_splsda_run: a dynamic branching target that runs the run_splsda() function for each dataset, using the results from individual_splsda_perf to guide the number of latent components to construct.

• filtered_set_slpsda: a target to retain from the original MultiDataSet object only features selected in each sPLS-DA run.

Examples

if (FALSE) { # \dontrun{
## in the _targets.R
library(moiraine)

list(
  ## add code here to load the different datasets

  ## the following target creates a MultiDataSet object from previously
  ## created omics sets (geno_set, trans_set, etc)
  tar_target(
    mo_set,
    create_multiomics_set(geno_set, trans_set, metabo_set, pheno_set)
  ),
  feature_preselection_splsda_factory(
    mo_set,
    group = "outcome_group",
    to_keep_ns = c("rnaseq" = 1000, "metabolome" = 500),
    filtered_set_target_name = "mo_set_filtered",
    folds = 10 ## example of an argument passed to perf_splsda
  ),

  ## Another example using to_keep_props
  feature_preselection_splsda_factory(
    mo_set,
    group = "outcome_group",
    to_keep_ns = NULL,
    to_keep_props = c("rnaseq" = 0.3, "metabolome" = 0.5),
    filtered_set_target_name = "mo_set_filtered",
    folds = 10 ## example of an argument passed to perf_splsda
  )
)
} # }