edgeR: topSpliceDGE – R documentation

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edgeR

topSpliceDGE

Top table of differentially spliced genes or exons

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