predict,biosign-method {biosigner} | R Documentation

## Predict method for 'biosign' signature objects

### Description

This function predicts values based upon `biosign` classifiers trained on the 'S' signature

### Usage

    ## S4 method for signature 'biosign'
    predict(object, newdata, tierMaxC = "S", ...)

### Arguments

`object` | An S4 object of class `biosign`, created by `biosign` function.
`newdata` | Either a data frame or a matrix, containing numeric columns only, with column names identical to the 'x' used for model training with 'biosign'.
`tierMaxC` | Character: Maximum level of tiers to display: Either 'S'or 'A'.
`...` | Currently not used.

### Value

Data frame with the predictions for each classifier as factor columns.

### Author(s)

Philippe Rinaudo and Etienne Thevenot (CEA)

### Examples

    ## loading the diaplasma dataset

    data(diaplasma)
    attach(diaplasma)

    ## restricting to a smaller dataset for this example

    featureSelVl <- variableMetadata[, "mzmed"] >= 490 & variableMetadata[, "mzmed"] < 500
    dataMatrix <- dataMatrix[, featureSelVl]
    variableMetadata <- variableMetadata[featureSelVl, ]

    ## training the classifiers
    ## a bootI = 5 number of bootstraps is used for this example
    ## we recommend to keep the default bootI = 50 value for your analyzes

    set.seed(123)
    diaSign <- biosign(dataMatrix, sampleMetadata[, "type"], bootI = 5)

    ## fitted values (for the subsets restricted to the 'S' signatures)
    sFitDF <- predict(diaSign)

    ## confusion tables
    print(lapply(sFitDF, function(predFc) table(actual = sampleMetadata[,
    "type"], predicted = predFc)))

    ## balanced accuracies
    sapply(sFitDF, function(predFc) { conf <- table(sampleMetadata[,
    "type"], predFc)
    conf <- sweep(conf, 1, rowSums(conf), "/")
    mean(diag(conf))
    })
    ## note that these values are slightly different from the accuracies
    ## returned by biosign because the latter are computed by using the
    ## resampling scheme selected by the bootI or crossvalI arguments
    getAccuracyMN(diaSign)["S", ]

    detach(diaplasma)

[Package biosigner version 1.10.0 Index]