Top table of differentially spliced genes or exons

Share:

Description

Top table ranking the most differentially spliced genes or exons.

Usage

1
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.

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.