metamorphr (version 0.3.0)

impute_nipals: Impute missing values using NIPALS PCA

Description

One of several PCA-based imputation methods. Basically a wrapper around pcaMethods::pca(method = "nipals"). For a detailed discussion, see the vignette("pcaMethods") and vignette("missingValues", "pcaMethods") as well as the References section.

Important Note

impute_nipals() depends on the pcaMethods package from Bioconductor. If metamorphr was installed via install.packages(), dependencies from Bioconductor were not automatically installed. When impute_nipals() is called without the pcaMethods package installed, you should be asked if you want to install pak and pcaMethods. If you want to use impute_nipals() you have to install those. In case you run into trouble with the automatic installation, please install pcaMethods manually. See pcaMethods – a Bioconductor package providing PCA methods for incomplete data for instructions on manual installation.

Usage

impute_nipals(data, n_pcs = 2, center = TRUE, scale = "none", direction = 2)

Value

A tibble with imputed missing values.

Arguments

data

A tidy tibble created by read_featuretable.

n_pcs

The number of PCs to calculate.

center

Should data be mean centered? See prep for details.

scale

Should data be scaled? See prep for details.

direction

Either 1 or 2. 1 runs a PCA on a matrix with samples in columns and features in rows and 2 runs a PCA on a matrix with features in columns and samples in rows. Both are valid according to this discussion on GitHub but give different results.

References

• H. R. Wolfram Stacklies, 2017, DOI 10.18129/B9.BIOC.PCAMETHODS.

• W. Stacklies, H. Redestig, M. Scholz, D. Walther, J. Selbig, Bioinformatics 2007, 23, 1164–1167, DOI 10.1093/bioinformatics/btm069.

Examples

toy_metaboscape %>%
  impute_nipals()