predictTssOverlap-methods: predictTssOverlap

In transcriptR: An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification

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)

transcriptR documentation built on Nov. 8, 2020, 8:12 p.m.