pca {pcaMethods} | R Documentation

## Perform principal component analysis

### Description

Perform PCA on a numeric matrix for visualisation, information extraction and missing value imputation.

### Usage

    pca(object, method, nPcs = 2, scale = c("none", "pareto", "vector", "uv"),
      center = TRUE, completeObs = TRUE, subset = NULL, cv = c("none",
      "q2"), ...)

### Arguments

`object` | Numerical matrix with (or an object coercible to such) with samples in rows and variables as columns. Also takes `ExpressionSet` in which case the transposed expression matrix is used. Can also be a data frame in which case all numberic variables are used to fit the PCA.
`method` | One of the methods reported by `listPcaMethods()`. Can be left missing in which case the `svd` PCA is chosen for data wihout missing values and `nipalsPca` for data with missing values
`nPcs` | Number of principal components to calculate.
`scale` | Scaling, see `prep`.
`center` | Centering, see `prep`.
`completeObs` | Sets the `completeObs` slot on the resulting `pcaRes` object containing the original data with but with all NAs replaced with the estimates.
`subset` | A subset of variables to use for calculating the model. Can be column names or indices.
`cv` | character naming a the type of cross-validation to be performed.
`...` | Arguments to `prep`, the chosen pca method and `Q2`.

### Details

This method is wrapper function for the following set of pca methods:

svd:

  Uses classical `prcomp`. See documentation for `svdPca`.

nipals:

  An iterative method capable of handling small amounts of missing values. See documentation for `nipalsPca`.

rnipals:

  Same as nipals but implemented in R.

bpca:

  An iterative method using a Bayesian model to handle missing values. See documentation for `bpca`.

ppca:

  An iterative method using a probabilistic model to handle missing values. See documentation for `ppca`.

svdImpute:

  Uses expectation maximation to perform SVD PCA on incomplete data. See documentation for `svdImpute`.

Scaling and centering is part of the PCA model and handled by `prep`.

### Value

A `pcaRes` object.

### Author(s)

Wolfram Stacklies, Henning Redestig

### References

Wold, H. (1966) Estimation of principal components and related models by iterative least squares. In Multivariate Analysis (Ed., P.R. Krishnaiah), Academic Press, NY, 391-420.

Shigeyuki Oba, Masa-aki Sato, Ichiro Takemasa, Morito Monden, Ken-ichi Matsubara and Shin Ishii. A Bayesian missing value estimation method for gene expression profile data. Bioinformatics, 19(16):2088-2096, Nov 2003.

Troyanskaya O. and Cantor M. and Sherlock G. and Brown P. and Hastie T. and Tibshirani R. and Botstein D. and Altman RB. - Missing value estimation methods for DNA microarrays. Bioinformatics. 2001 Jun;17(6):520-5.

### See Also

`prcomp`, `princomp`, `nipalsPca`, `svdPca`

### Examples

    data(iris)
    ##  Usually some kind of scaling is appropriate
    pcIr <- pca(iris, method="svd", nPcs=2)
    pcIr <- pca(iris, method="nipals", nPcs=3, cv="q2")
    ## Get a short summary on the calculated model
    summary(pcIr)
    plot(pcIr)
    ## Scores and loadings plot
    slplot(pcIr, sl=as.character(iris[,5]))

    ## use an expressionset and ggplot
    data(sample.ExpressionSet)
    pc <- pca(sample.ExpressionSet)
    df <- merge(scores(pc), pData(sample.ExpressionSet), by=0)
    library(ggplot2)
    ggplot(df, aes(PC1, PC2, shape=sex, color=type)) +
      geom_point() +
      xlab(paste("PC1", pc@R2[1] * 100, "% of variance")) +
      ylab(paste("PC2", pc@R2[2] * 100, "% of variance"))

[Package pcaMethods version 1.72.0 Index]