spliceVariants(y, geneID, dispersion=NULL, group=NULL, estimate.genewise.disp=TRUE,
trace=FALSE)
DGEList
object with (at least) elements counts
(table of counts summarized at the exon level) and samples
(data frame containing information about experimental group, library size and normalization factor for the library size). Each row of y
should represent one exon.y
, which provides the gene identifier for each exon in y
. These identifiers are used to group the relevant exons into genes for the gene-level analysis of splice variation.y
) belongs. If NULL
(default) the function will try to extract if from y
, which only works if y
is a DGEList
object.dispersion
argument is NULL
?FALSE
.spliceVariants
returns a DGEExact
object, which contains a table of results for the test of differential splicing between experimental groups (alternative exon usage), a data frame containing the gene identifiers for which results were obtained and the dispersion estimate(s) used in the statistical models and testing.topTags
can be used to display the results of spliceVariants
with genes ranked by evidence for splice variation.estimateExonGenewiseDisp
for more information about estimating genewise dispersion values from exon-level counts. DGEList
for more information about the DGEList
class. topTags
for more information on displaying ranked results from spliceVariants
. estimateCommonDisp
and related functions for estimating the dispersion parameter for the negative binomial model.# generate exon counts from NB, create list object
y<-matrix(rnbinom(40,size=1,mu=10),nrow=10)
d<-DGEList(counts=y,group=rep(1:2,each=2))
genes <- rep(c("gene.1","gene.2"), each=5)
disp <- 0.2
spliceVariants(d, genes, disp)
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