topSpliceDGE: Top table of differentially spliced genes or exons

In edgeR: Empirical Analysis of Digital Gene Expression Data in R

Description

Top table ranking the most differentially spliced genes or exons.

Usage

topSpliceDGE(lrt, test="Simes", number=10, FDR=1)

Arguments

lrt	DGELRT object produced by diffSpliceDGE.
test	character string, possible values are "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.
number	integer, maximum number of rows to output.
FDR	numeric, only show exons or genes with false discovery rate less than this cutoff.

Details

Ranks genes or exons by evidence for differential splicing. The exon-level tests test for differences between each exon and all the exons for the same gene. The gene-level tests test for any differences in exon usage between experimental conditions.

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.

Value

A data.frame with any annotation columns found in lrt plus the following columns

NExons	number of exons if test="Simes" or "gene"
Gene.Exon	exon annotation if test="exon"
logFC	log-fold change of one exon vs all the exons for the same gene (if test="exon")
exon.LR	LR-statistics for exons (if test="exon" and the object for diffSpliceDGE was produced by glmFit)
exon.F	F-statistics for exons (if test="exon" and the object for diffSpliceDGE was produced by glmQLFit)
gene.LR	LR-statistics for genes (if test="gene" and the object for diffSpliceDGE was produced by glmFit)
gene.F	F-statistics for genes (if test="gene" and the object for diffSpliceDGE was produced by glmQLFit)
P.Value	p-value
FDR	false discovery rate

Author(s)

Yunshun Chen and Gordon Smyth

See Also

diffSpliceDGE.

edgeR documentation built on Jan. 16, 2021, 2:03 a.m.