IsoDataSet-initialize: IsoDataSet object constructor.

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

Description

initialize creates an IsoDataSet object with the specified isoform expression counts.

Usage

## S4 method for signature 'IsoDataSet'
initialize(.Object, isoCounts, experimentData, colName,
    geneIso, BPPARAM = bpparam())

Arguments

.Object	IsoDataSet class object.
isoCounts	Matrix having the expression counts at the isoform level. Isoforms must be in rows and samples in columns. Rownames and colnames must be defined with isoform and samples names, respectively.
experimentData	Data.frame specifying metadata related to the experiment. Its rows must be the samples and experimental factors should be arranged on its columns.
colName	Character indicating the name of the column in the design matrix to be considered for mean expression calculations per experimental condition and differential expression test.
geneIso	Data.frame containing the relationship between isoforms and genes. It must contain two columns, named as 'gene_id' and 'isoform_id'. Its isoforms should be the same specified in the isoCounts matrix.
BPPARAM	An optional BiocParallelParam instance defining the parallel back-end to be used during evaluation.

Value

IsoDataSet object.

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, NBTest, buildData, buildLowExpIdx, designMatrix, geneIso, isoCountsData, myIsoDataSet

Examples

## Data loading
data(isoCounts, package="NBSplice")
data(designMatrix, package="NBSplice")
data(geneIso, package="NBSplice")

## Arguments definition
colName<-"condition"

## Constructor calling
myIsoDataSet<-IsoDataSet(isoCounts, designMatrix, colName, geneIso)

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