edgeR (version 3.8.6)

topSpliceDGE: Top table of differentially spliced genes or exons

Description

Top table ranking the most differentially spliced genes or exons.

Usage

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

Arguments

lrt

DGELRT object produced by diffSpliceDGE.

level

character string, should the table be by "exon" or by "gene".

gene.test

character string, choice for the gene-level p-values. Possible values are "Simes" and "F".

number

integer, maximum number of rows to output.

FDR

numeric, only show exons or genes with false discovery rate less than this cutoff.

Value

fit plus the following columns

NExons

number of exons if level="gene"

Gene.Exon

exon annotation if level="exon"

logFC

log-fold change of one exon vs all the exons for the same gene (if level="exon")

F

F-statistics for exons if level="exon"

P.Value

p-value

FDR

false discovery rate

Details

Ranks exons or genes by p-values.