Classify {signeR} | R Documentation |
Classify: Assign unknown samples to previously defined groups.
## 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, ...)
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: |
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). |
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. |
# 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")