IsoDataSet {NBSplice} | R Documentation |
IsoDataSet
creates an object to store expression counts at
isoform and gene level, the relationship between those, the experiment data
and the formula to be used for models fitting required to evaluate
differential splicing.
IsoDataSet(isoCounts, experimentData, colName, geneIso, BPPARAM = bpparam())
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 differential splicing analysis. |
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. |
IsoDataSet object.
see full example in IsoDataSet-class
Gabriela A. Merino merino.gabriela33@gmail.com, and Elmer A. Fernandez efernandez@bdmg.com.ar
Other IsoDataSet: IsoDataSet-class
,
NBTest
, buildData
,
buildLowExpIdx
, designMatrix
,
geneIso
, initialize
,
isoCountsData
, myIsoDataSet
## 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)