IsoDataSet-NBTest: Differential splicing analysis.

In gamerino/NBSplice: Negative Binomial Models to detect Differential Splicing

Description

NBTest is the main function of NBSplice. It fits the negative binomial models for all genes and performs the corresponding hypothesis tests to evaluate the occurrence of differential splicing.

Usage

NBTest(object, colName = "condition", test = c("F", "Chisq"),
    contrast = c(levels(expData(object)[,colName])[seq_len(2)]),
    BPPARAM = bpparam())

## S4 method for signature 'IsoDataSet'
NBTest(object, colName = "condition", test = c("F",
    "Chisq"), contrast = c(levels(expData(object)[,colName])[seq_len(2)]),
    BPPARAM = bpparam())

Arguments

object	IsoDataSet class object.
colName	Character indicating the name of the column in the design matrix to be considered for mean expression calculations per experimental condition.
test	Character indicating the name of the distribution to assume for linear hypothesis statistic. Could be "F" or "chisq".
contrast	Character vector with the names of the two levels of the experimental factor to be contrasted.
BPPARAM	An optional BiocParallelParam instance defining the parallel back-end to be used during evaluation.

Value

A NBSpliceRes object with the obtained results.

Note

see full example in IsoDataSet-class

Author(s)

Gabriela A. Merino [e-mail] and Elmer A. Fernandez [e-mail]

See Also

IsoDataSet

Other IsoDataSet: IsoDataSet-class, IsoDataSet, buildData, buildLowExpIdx, designMatrix, geneIso, initialize, isoCountsData, myIsoDataSet

Examples

## Data loading
data(myIsoDataSet, package="NBSplice")

## Identificating Low expressed Isoforms
myIsoDataSet<-buildLowExpIdx(myIsoDataSet)

##Arguments definition
colName<-"condition"
test<-"F"

## Differential splicing test
myDSResults<-NBTest(myIsoDataSet, colName, test)

gamerino/NBSplice documentation built on Sept. 10, 2021, 10:21 p.m.