isoCountsData: An example of an isoform counts matrix helpful to demonstrate...

In NBSplice: Negative Binomial Models to detect Differential Splicing

Description

A non-real dataset containing isoform expression counts of a synthetic dataset where several differential splicing changes were simulated and controlled.

Format

A data.frame object

Details

Isoform expression matrix where isoforms are in rows and samples in columns. Samples 'C1R1', 'C1R2', 'C1R3' and 'C1R4' are from Normal condition, whereas 'C2R1', 'C2R2', 'C2R3' and 'C2R4' are from Tumor condition. The matrix is a subset of an expression matrix obtained from a simulated RNA-seq experiment where differential splicing is controlled, used for NBSplice evaluation. The full expression matrix could be dowloaded from the GitHub respository https://github.com/gamerino/NBSpliceSuppInformation. In particular, the file expressionMatrixSim1.RData from the Data/sim1 folder was used here. The metadata information was obtained from the isoInfoSim1.RData file, stored in the same folder. For NBSplice package demonstration, a subset of 500 genes were selected doing genes<-unique(iso_info$gene_id) set.seed(12345) selectedGenes<-sample(genes, 500) isoInfo<-iso_info[iso_info$gene_id geneIso<-isoInfo[, c("gene_id", "transcript_id")] colnames(geneIso)[2]<-"isoform_id" isoCounts<-iso_cm[isoInfo$transcript_id,]

The isoCounts matrix, the geneIso and the designMatrix data.frames are provided with NBSplice.

Author(s)

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

Source

see IsoDataSet-class

See Also

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

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