# topTags

From edgeR v3.14.0
by Yunshun Chen

##### Table of the Top Differentially Expressed Tags

Extracts the top DE tags in a data frame for a given pair of groups, ranked by p-value or absolute log-fold change.

- Keywords
- algebra

##### Usage

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

##### Arguments

- object
- a
`DGEExact`

object (output from`exactTest`

) or a`DGELRT`

object (output from`glmLRT`

), containing the (at least) the elements`table`

: a data frame containing the log-concentration (i.e. expression level), the log-fold change in expression between the two groups/conditions and the p-value for differential expression, for each tag. If it is a`DGEExact`

object, then`topTags`

will also use the`comparison`

element, which is a vector giving the two experimental groups/conditions being compared. The object may contain other elements that are not used by`topTags`

. - n
- scalar, number of tags to display/return
- adjust.method
- character string stating the method used to adjust p-values for multiple testing, passed on to
`p.adjust`

- sort.by
- character string, should the top tags be sorted by p-value (
`"PValue"`

), by absolute log-fold change (`"logFC"`

), or not sorted (`"none"`

). - p.value
- cutoff value for adjusted p-values. Only tags with lower p-values are listed.

##### Value

- an object of class
- table
- a data frame containing the elements
`logFC`

, the log-abundance ratio, i.e. fold change, for each tag in the two groups being compared,`logCPM`

, the log-average concentration/abundance for each tag in the two groups being compared,`PValue`

, exact p-value for differential expression using the NB model,`FDR`

, the p-value adjusted for multiple testing as found using`p.adjust`

using the method specified. - adjust.method
- character string stating the method used to adjust p-values for multiple testing.
- comparison
- a vector giving the names of the two groups being compared.
- test
- character string stating the name of the test. The dimensions, row names and column names of a

`TopTags`

containing the following elements for the top `n`

most differentially expressed tags as determined by `sort.by`

:`TopTags`

object are defined by those of `table`

, see `dim.TopTags`

or `dimnames.TopTags`

.`TopTags`

objects also have a `show`

method so that printing produces a compact summary of their contents.Note that the terms `tag' and `gene' are synonymous here. The function is only named as `Tags' for historical reasons.
##### References

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

Analogous to `topTable`

in the limma package.

##### 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")
```

*Documentation reproduced from package edgeR, version 3.14.0, License: GPL (>=2)*

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