predictTssOverlap {transcriptR} | R Documentation

## predictTssOverlap

### Description

The function classifies ChIP-seq peaks on gene associated and background using classification model based on a logistic regression.

### Usage

    predictTssOverlap(object, feature, p = 0.8)

    ## S4 method for signature 'ChipDataSet'
    predictTssOverlap(object, feature, p = 0.8)

### Arguments

`object` | A `ChipDataSet` object.
`feature` | `Character`. Specify feature(s) that are be used as predictors in the classification model. By default, all the features stored in the `ChipDataSet` object will be used.
`p` | `Numeric`. The proportion of data that is used to train the model. Default: 0.8.

### Details

In order to improve the accuracy of the model the data is internally partitioned into a training and testing data sets. A repeated 10-Fold Cross-Validation is used to calculate performance measures on the training data set and to prevent over-fitting.

The model fit and validation is internally acomplised by the functions implemented in the caret package.

### Value

The slot `tssOverlapPrediction` of the provided `TranscriptionDataSet` object will be updated by the the following elements: 'predicted.tssOverlap', 'confusionMatrix', 'logFitSummary' and 'roc'.

### Author(s)

Armen R. Karapetyan

### See Also

`ChipDataSet` `constructCDS` caret

### Examples

    ### Load ChipDataSet object
    data(cds)

    predictTssOverlap(object = cds, feature = "pileup", p = 0.75)

    ### View a short summary of the gene associated peaks prediction
    cds

    ### View peaks and associated prediction
    getPeaks(cds)

[Package transcriptR version 1.12.0 Index]