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Performs sPLS-DA on omics dataset from MultiDataSet object

Source: R/prefiltering.R
run_splsda.Rd

Performs a sPLS-DA (implemented in the mixOmics) package on a omics dataset from a MultiDataSet object. This is intended for feature preselection in the omics dataset (see get_filtered_dataset_splsda()).

Usage

run_splsda(
  splsda_input,
  perf_res,
  to_keep_n = NULL,
  to_keep_prop = NULL,
  ncomp = NULL,
  seed = NULL
)

Arguments

splsda_input

Input for the sPLS-DA functions from mixOmics, created with get_input_splsda().

perf_res

Result of the perf_splsda() function. If not supplied, sPLS-DA will be run on dataset specified by argument dataset_name with number of latent components specified by argument comp.

to_keep_n

Integer, the number of features to retain in the dataset. Should be less than the number of features in the dataset. If NULL or NA, to_keep_prop will be used instead.

to_keep_prop

Numeric, the proportion of features to retain in the dataset. Will be ignored if to_keep_n is supplied. Value should be > 0 and < 1.

ncomp

Integer, number of latent components to construct. Ignored if perf_res is supplied. Default value is NULL.

seed

Integer, seed to use. Default is NULL, i.e. no seed is set inside the function.

Value

A list as per the output of the mixOmics::splsda() function.

Details

This function uses the mixOmics::plsda() function from the mixOmics package. Note that the sPLS-DA method can select the same feature for several latent components, so the number of features retained for a dataset might be less than the number specified in the to_keep_n argument.