topSpliceDGE(lrt, test="Simes", number=10, FDR=1)DGELRT object produced by diffSpliceDGE."Simes", "gene" or "exon".
"exon" gives exon-level tests for each exon.
"gene" gives gene-level tests for each gene.
"Simes" gives genewise p-values derived from the exon-level tests after Simes adjustment for each gene.lrt plus the following columns
test="Simes" or "gene"test="exon"test="exon")test="exon" and the object for diffSpliceDGE was produced by glmFit)test="exon" and the object for diffSpliceDGE was produced by glmQLFit)test="gene" and the object for diffSpliceDGE was produced by glmFit)test="gene" and the object for diffSpliceDGE was produced by glmQLFit)The Simes method processes the exon-level p-values to give an overall call of differential splicing for each gene. It returns the minimum Simes-adjusted p-values for each gene.
The gene-level tests are likely to be powerful for genes in which several exons are differentially splices. The Simes p-values is likely to be more powerful when only a minority of the exons for a gene are differentially spliced. The exon-level tests are not recommended for formal error rate control.
diffSpliceDGE.