Top tables of differentially expressed genes.

topTables(object, ...)

# S4 method for DESeqAnalysis
topTables(object, results, n = 10L,
  lfcShrink = TRUE)

Arguments

object

Object.

results

character(1) or integer(1). Name or position of DESeqResults.

n

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

lfcShrink

logical(1). Use shrunken log2 fold change (LFC) values.

...

Additional arguments.

Value

kable. Markdown tables.

Examples

data(deseq) ## DESeqAnalysis ==== topTables(deseq, results = 1L, n = 5L)
#> condition_B_vs_A (shrunken LFC)
#> Returning with the sample names unmodified.
#> Joining row annotations.
#> 171 differentially expressed genes detected.
#> 84 upregulated genes detected.
#> 87 downregulated genes detected.
#> #> #> |rowname |baseMean |lfc |padj |geneID |geneName |geneBiotype | #> |:-------|:--------|:----|:--------|:---------------|:--------|:--------------| #> |gene095 |123 |2.36 |1.86e-09 |ENSG00000005381 |MPO |protein_coding | #> |gene334 |72 |2.85 |4.57e-09 |ENSG00000013392 |RWDD2A |protein_coding | #> |gene323 |195 |1.99 |5.64e-09 |ENSG00000012963 |UBR7 |protein_coding | #> |gene494 |113 |1.76 |6.55e-09 |ENSG00000032389 |EIPR1 |protein_coding | #> |gene391 |901 |1.62 |4.54e-08 |ENSG00000019485 |PRDM11 |protein_coding | #> #> #> |rowname |baseMean |lfc |padj |geneID |geneName |geneBiotype | #> |:-------|:--------|:-----|:--------|:---------------|:--------|:--------------| #> |gene427 |44 |-2.90 |3.20e-14 |ENSG00000023318 |ERP44 |protein_coding | #> |gene419 |28 |-2.99 |3.75e-11 |ENSG00000022567 |SLC45A4 |protein_coding | #> |gene352 |26 |-2.86 |4.53e-08 |ENSG00000014824 |SLC30A9 |protein_coding | #> |gene497 |48 |-2.17 |6.60e-06 |ENSG00000033011 |ALG1 |protein_coding | #> |gene004 |81 |-1.94 |2.77e-05 |ENSG00000000457 |SCYL3 |protein_coding |