poplin_reduced: Dimension-reduced data methods

In jaehyunjoo/poplin: LC/MS Metabolomics Data Processing Utilities

Description

Methods to get or set dimension reduction results in a poplin object. These methods are intended to store and retrieve low-dimensional representation (e.g., PCA, PLS-DA) of LC/MS data sets.

Getters

In the code snippets below, x is a poplin object.

poplin_reduced_names(x):

Return the names of all dimension-reduced data sets.

poplin_reduced_list(x):

Retrieves a named List of matrices containing one or more dimension-reduced data. Each entry is a matrix with the same number of rows as ncol(x).

poplin_reduced(x, type):

Retrieves a matrix of low-dimensional representation. type is either a string specifying the name of data set to retrieve or an integer specifying the index of the desired data sets, defaulting to the first entry if missing.

Setters

poplin_reduced_names(x) <- value:

value must be a character vector to be assigned for the names of dimension-reduced data sets.

poplin_reduced_list(x) <- value:

value is expected to be a named List of matrices. If the result already exists, it will be replaced. If value is NULL, any existing result will be removed.

poplin_reduced(x, type) <- value:

value is expected to be a matrix. type determines how the result is assigned:

• integer: it must be within the range of existing results. value will replace the result at that index.

• character: if the result exists with this name, it will be replaced with value. Otherwise a new result with this name will be appended.

• missing: value will be assigned to the first entry.

If value is NULL, the result corresponding to type will be removed.

See Also

poplin_raw, poplin_data

Examples

data(faahko_poplin)
poplin_reduced_list(faahko_poplin)
poplin_reduced_names(faahko_poplin)
poplin_reduced(faahko_poplin)
poplin_reduced(faahko_poplin, 2)
poplin_reduced(faahko_poplin, "pca")

jaehyunjoo/poplin documentation built on Jan. 8, 2022, 1:13 a.m.