IsoDataSet-buildLowExpIdx: IsoDataSet low expressed isoforms detection.

In NBSplice: Negative Binomial Models to detect Differential Splicing

Description

buildLowExpIdx identifies low expressed isoforms and stores their indexes to facilitate their identification. Low expression is defined combining absolute and relative expression thresholds.

Usage

buildLowExpIdx(object, colName = "condition", ratioThres = 0.01,
    countThres = 1, BPPARAM = bpparam())
## S4 method for signature 'IsoDataSet'
buildLowExpIdx(object, colName = "condition",
    ratioThres = 0.01, countThres = 1, BPPARAM = bpparam())

Arguments

object	IsoDataSet class object.
colName	Character indicating the name of the column in the design matrix to be considered for differential expression analysis.
ratioThres	Numeric indicating the minimum isoform's relative expression value admitted. If one isoform had expression lower than this threshold in at least one sample, thus it will be ignored for further analysis.
countThres	Numeric indicating the isoform's expression threshold. If one isoform showed a mean expression value lower than this threshold in at least one experimental condition, thus it will be ignored for further analysis.
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, designMatrix, geneIso, initialize, isoCountsData, myIsoDataSet

Examples

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

## Identification of low expressed isoforms
myIsoDataSet<-buildLowExpIdx(myIsoDataSet)

NBSplice documentation built on Nov. 8, 2020, 8:07 p.m.