NBTest {NBSplice} | R Documentation |
NBTest
is the main function of NBSplice. It fits the negative binomial
models for all genes and performs the corresponding hypothesis tests to
evaluate the occurrence of differential splicing.
NBTest(object, colName = "condition", test = c("F", "Chisq"), contrast = c(levels(expData(object)[,colName])[seq_len(2)]), BPPARAM = bpparam()) ## S4 method for signature 'IsoDataSet' NBTest(object, colName = "condition", test = c("F", "Chisq"), contrast = c(levels(expData(object)[,colName])[seq_len(2)]), BPPARAM = bpparam())
object |
IsoDataSet class object. |
colName |
Character indicating the name of the column in the design matrix to be considered for mean expression calculations per experimental condition. |
test |
Character indicating the name of the distribution to assume for linear hypothesis statistic. Could be "F" or "chisq". |
contrast |
Character vector with the names of the two levels of the experimental factor to be contrasted. |
BPPARAM |
An optional BiocParallelParam instance defining the parallel back-end to be used during evaluation. |
A NBSpliceRes object with the obtained results.
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
, buildData
,
buildLowExpIdx
, designMatrix
,
geneIso
, initialize
,
isoCountsData
, myIsoDataSet
## Data loading data(myIsoDataSet, package="NBSplice") ## Identificating Low expressed Isoforms myIsoDataSet<-buildLowExpIdx(myIsoDataSet) ##Arguments definition colName<-"condition" test<-"F" ## Differential splicing test myDSResults<-NBTest(myIsoDataSet, colName, test)