topTags {edgeR} | R Documentation

## Table of the Top Differentially Expressed Genes/Tags

### Description

Extracts the most differentially expressed genes (or sequence tags) from a test object, ranked either by p-value or by absolute log-fold-change.

### Usage

    topTags(object, n = 10, adjust.method = "BH", sort.by = "PValue", p.value = 1)

### Arguments

`object` | a `DGEExact` or `DGELRT` object containing test statistics and p-values. Usually created by `exactTest`, `glmLRT`, `glmTreat` or `glmQLFTest`.
`n` | integer, maximum number of genes/tags to return.
`adjust.method` | character string specifying the method used to adjust p-values for multiple testing. See `p.adjust` for possible values.
`sort.by` | character string specifying the sort method. Possibilities are `"PValue"` for p-value, `"logFC"` for absolute log-fold change or `"none"` for no sorting.
`p.value` | numeric cutoff value for adjusted p-values. Only tags with adjusted p-values equal or lower than specified are returned.

### Details

This function is closely analogous to the `topTable` function in the limma package. It accepts a test statistic object created by any of the edgeR functions `exactTest`, `glmLRT`, `glmTreat` or `glmQLFTest` and extracts a readable data.frame of the most differentially expressed genes. The data.frame collates the annotation and differential expression statistics for the top genes. The data.frame is wrapped in a `TopTags` output object that records the test statistic used and the multiple testing adjustment method.

`TopTags` objects will return dimensions and hence functions such as `dim`, `nrow` or `ncol` are defined on them. `TopTags` objects also have a `show` method so that printing produces a compact summary of their contents.

`topTags` permits ranking by fold-change but the authors do not recommend fold-change ranking or fold-change cutoffs for routine RNA-seq analysis. The p-value ranking is intended to more biologically meaningful, especially if the p-values were computed using `glmTreat`.

### Value

An object of class `TopTags`, which is a list-based class with the following components:

`table` | a data.frame containing differential expression results for the top genes in sorted order. The number of rows is the smaller of `n` and the number of genes with adjusted p-value less than or equal to `p.value`. The data.frame includes all the annotation columns from `object$genes` and all statistic columns from `object$table` plus one of:
`FDR`: | false discovery rate (only when `adjust.method` is `"BH"`, `"BY"` or `"fdr"`)
`FWER`: | family-wise error rate (only when `adjust.method` is `"holm"`, `"hochberg"`, `"hommel"` or `"bonferroni"`).
`adjust.method` | character string specifying the method used to adjust p-values for multiple testing, same as input argument.
`comparison` | character vector giving the names of the two groups being compared (for `DGEExact` objects) or the glm contrast being tested (for `DGELRT` objects).
`test` | character string stating the name of the test.

### Note

The terms ‘tag’ and ‘gene’ are used synonymously on this page and refer to the rows of `object`. In general, the rows might be genes, sequence tags, transcripts, exons or whatever type of genomic feature is appropriate for the analysis at hand.

### Author(s)

Mark Robinson, Davis McCarthy, Yunshun Chen, Gordon Smyth

### References

Chen Y, Lun ATL, and Smyth, GK (2016). From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline. F1000Research 5, 1438. http://f1000research.com/articles/5-1438

McCarthy, DJ, Chen, Y, Smyth, GK (2012). Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Research 40, 4288-4297. doi: 10.1093/nar/gks042

Robinson MD, Smyth GK (2008). Small-sample estimation of negative binomial dispersion, with applications to SAGE data. Biostatistics 9, 321-332.

Robinson MD, Smyth GK (2007). Moderated statistical tests for assessing differences in tag abundance. Bioinformatics 23, 2881-2887.

### See Also

`exactTest`, `glmLRT`, `glmTreat`, `glmQLFTest`, `dim.TopTags`, `p.adjust`.

### Examples

    # generate raw counts from NB, create list object
    y <- matrix(rnbinom(80,size=1,mu=10),nrow=20)
    d <- DGEList(counts=y,group=rep(1:2,each=2),lib.size=rep(c(1000:1001),2))
    rownames(d$counts) <- paste("gene",1:nrow(d$counts),sep=".")

    # estimate common dispersion and find differences in expression
    # here we demonstrate the 'exact' methods, but the use of topTags is
    # the same for a GLM analysis
    d <- estimateCommonDisp(d)
    de <- exactTest(d)

    # look at top 10
    topTags(de)
    # Can specify how many genes to view
    tp <- topTags(de, n=15)
    # Here we view top 15
    tp
    # Or order by fold change instead
    topTags(de,sort.by="logFC")

[Package edgeR version 3.36.0 Index]