R/NBSplice-isoCounts.R

In NBSplice: Negative Binomial Models to detect Differential Splicing

#'An example of an isoform counts matrix helpful to demonstrate the use of
#'the NBSplice R package.
#'
#'A non-real dataset containing isoform expression counts of a synthetic 
#'dataset where several differential splicing changes were simulated and
#'controlled. 
#'
#'\describe{
#'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 %in% selectedGenes,]
#'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.
#'}
#'
#'@include NBSpliceRes-plotGeneResults.R
#'@docType data
#'@format A data.frame object
#'@source see \code{\link{IsoDataSet-class}}
#'@name isoCountsData
#'@family IsoDataSet
#'@author Gabriela A. Merino \email{merino.gabriela33@@gmail.com} and 
#'Elmer A. Fernandez \email{efernandez@bdmg.com.ar}
NULL