IsoDataSet-buildLowExpIdx: IsoDataSet low expressed isoforms detection.

Description Usage Arguments Value Note Author(s) See Also Examples

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

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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 merino.gabriela33@gmail.com and Elmer A. Fernandez efernandez@bdmg.com.ar

See Also

IsoDataSet

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

Examples

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

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

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