initialize {NBSplice} | R Documentation |
initialize
creates an IsoDataSet object with the specified isoform
expression counts.
## S4 method for signature 'IsoDataSet' initialize(.Object, isoCounts, experimentData, colName, geneIso, BPPARAM = bpparam())
.Object |
IsoDataSet class object. |
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 mean expression calculations per experimental condition and differential expression test. |
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
,
IsoDataSet
, NBTest
,
buildData
, buildLowExpIdx
,
designMatrix
, geneIso
,
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)