Classify {signeR} | R Documentation

## Classify unknown samples

### Description

Classify: Assign unknown samples to previously defined groups.

### Usage

    ## S4 method for signature 'SignExp,character'
    Classify(signexp_obj, labels, method="knn",
        k=3, weights=NA, plot_to_file=FALSE, file="Classification_barplot.pdf",
        colors=NA_character_, min_agree=0.75, ...)

### Arguments

`signexp_obj` | A SignExp object returned by signeR function.
`labels` | Sample labels. Every sample labeled as NA will be classified according to its mutational profile and the profiles of labeled samples.
`method` | Classification algorithm used. Default is k-Nearest Neighbors (kNN). Any other algorithm may be used, as long as it is customized to satisfy the following conditions: Input: a matrix of labeled samples, with one sample per line and one feature per column; a matrix of unlabeled samples to classify, with the same structure; an array of labels, with one entry for each labeled sample. Output: an array of assigned labels, one for each unlabeled sample.
`k` | Number of nearest neighbors considered for classification, used only if method="kNN". Default is 3.
`weights` | Vector of weights applied to the signatures when performing classification. Default is NA, which leads all the signatures to have weight=1.
`plot_to_file` | Whether to save the plot to the file parameter. Default is FALSE.
`file` | File that will be generated with classification graphic output.
`colors` | Array of color names, one for each sample class. Colors will be recycled if the length of this array is less than the number of classes.
`min_agree` | Minimum frequency of agreement among individual classifications. Samples showing a frequency of agreement below this value are considered as "undefined". Default is 0.75.
`...` | additional parameters for classification algorithm (defined by "method" above).

### Value

A list with the following items:

`class` | The assigned classes for each unlabeled sample.
`freq` | Classification agreement for each unlabeled sample: the relative frequency of assignment of each sample to the group specified in "class".
`allfreqs` | Matrix with one column for each unlabeled sample and one row for each group label. Contains the assignment frequencies of each sample to each group.

### Examples

    # assuming signatures is the return value of signeR()

    my_labels <- c("a","a",NA,"b","b",NA)
    Class <- Classify(signatures$SignExposures, labels=my_labels)

    # see also
    vignette(package="signeR")

[Package signeR version 1.12.0 Index]