Top tables of differentially expressed genes.

topTables(object, ...)

# S4 method for DESeqAnalysis
topTables(object, i, n = 10L)

# S4 method for DESeqResults
topTables(object, DESeqDataSet = NULL, n = 10L)

# S4 method for list
topTables(object, n = 10L, contrast = NULL)

Arguments

object

Object.

i

Indices specifying elements to extract or replace. Indices are numeric or character vectors, empty (missing), or NULL.

For more information:

help(topic = "Extract", package = "base")
n

integer(1). Number of genes (per direction) to report.

DESeqDataSet

DESeqDataSet or NULL.

contrast

character(1) or NULL. Contrast name.

...

Additional arguments.

Value

kable. Markdown tables.

Functions

  • topTables,list-method: Legacy support for tbl_df list returned from resultsTables(). This method is still supported because it is used in the F1000 v2 workflow paper. Otherwise, we now recommend using the DESeqAnalysis method directly.

Note

Updated 2021-02-10.

Examples

data(deseq) ## DESeqAnalysis ==== topTables(deseq, i = 1L, n = 5L)
#> → condition_B_vs_A (shrunken LFC)
#> 38 differentially expressed genes (alpha < 0.01)
#> 24 upregulated genes (alpha < 0.01)
#> 14 downregulated genes (alpha < 0.01)
#> #> #> Table: condition_B_vs_A (upregulated) #> #> | | baseMean|lfc |padj |broadClass |geneName |description | #> |:-------|--------:|:----|:--------|:----------|:--------|:--------------------------------------------------| #> |gene338 | 236|2.89 |3.79e-09 |coding |RNF14 |ring finger protein 14 | #> |gene214 | 474|2.00 |6.73e-07 |coding |AASS |aminoadipate-semialdehyde synthase | #> |gene028 | 83|2.60 |3.52e-06 |coding |HECW1 |HECT, C2 and WW domain containing E3 ubiquitin ... | #> |gene112 | 76|2.11 |9.52e-05 |coding |LAMP2 |lysosomal associated membrane protein 2 | #> |gene465 | 117|1.88 |9.52e-05 |coding |IFNGR1 |interferon gamma receptor 1 | #> #> #> Table: condition_B_vs_A (downregulated) #> #> | | baseMean|lfc |padj |broadClass |geneName |description | #> |:-------|--------:|:-----|:--------|:----------|:--------|:--------------------------------------------------| #> |gene380 | 61|-3.09 |6.73e-07 |coding |WWTR1 |WW domain containing transcription regulator 1 | #> |gene401 | 261|-1.96 |9.52e-05 |coding |MNAT1 |MNAT1 component of CDK activating kinase | #> |gene494 | 27|-3.36 |9.52e-05 |coding |EIPR1 |EARP complex and GARP complex interacting prote... | #> |gene119 | 83|-1.74 |2.92e-04 |coding |TMEM98 |transmembrane protein 98 | #> |gene232 | 6|-6.72 |2.96e-04 |coding |CSDE1 |cold shock domain containing E1 |
## DESeqResults 'resultsTables()' list ==== res <- results(deseq, i = 1L)
#> → condition_B_vs_A (shrunken LFC)
resTbl <- resultsTables(res, return = "tbl_df")
#> 38 differentially expressed genes (alpha < 0.01)
#> 24 upregulated genes (alpha < 0.01)
#> 14 downregulated genes (alpha < 0.01)
topTables(resTbl, n = 5L)
#> #> #> Table: upregulated #> #> | | baseMean|lfc |padj | #> |:-------|--------:|:----|:--------| #> |gene338 | 236|2.89 |3.79e-09 | #> |gene214 | 474|2.00 |6.73e-07 | #> |gene028 | 83|2.60 |3.52e-06 | #> |gene112 | 76|2.11 |9.52e-05 | #> |gene465 | 117|1.88 |9.52e-05 | #> #> #> Table: downregulated #> #> | | baseMean|lfc |padj | #> |:-------|--------:|:-----|:--------| #> |gene380 | 61|-3.09 |6.73e-07 | #> |gene401 | 261|-1.96 |9.52e-05 | #> |gene494 | 27|-3.36 |9.52e-05 | #> |gene119 | 83|-1.74 |2.92e-04 | #> |gene232 | 6|-6.72 |2.96e-04 |