Top tables of differentially expressed genes.

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

Arguments

object

Object.

results

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

n

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

Value

kable. Markdown tables.

Examples

data(deseq) ## DESeqAnalysis ==== topTables(deseq, results = 1L, n = 5L)
#> DESeqResults: 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.
#> #> #> |geneID |geneName |baseMean |lfc |padj |geneBiotype | #> |:---------------|:--------|:--------|:----|:--------|:--------------| #> |ENSG00000005381 |MPO |123 |2.36 |1.86e-09 |protein_coding | #> |ENSG00000013392 |RWDD2A |72 |2.85 |4.57e-09 |protein_coding | #> |ENSG00000012963 |UBR7 |195 |1.99 |5.64e-09 |protein_coding | #> |ENSG00000032389 |EIPR1 |113 |1.76 |6.55e-09 |protein_coding | #> |ENSG00000019485 |PRDM11 |901 |1.62 |4.54e-08 |protein_coding | #> #> #> |geneID |geneName |baseMean |lfc |padj |geneBiotype | #> |:---------------|:--------|:--------|:-----|:--------|:--------------| #> |ENSG00000023318 |ERP44 |44 |-2.90 |3.20e-14 |protein_coding | #> |ENSG00000022567 |SLC45A4 |28 |-2.99 |3.75e-11 |protein_coding | #> |ENSG00000014824 |SLC30A9 |26 |-2.86 |4.53e-08 |protein_coding | #> |ENSG00000033011 |ALG1 |48 |-2.17 |6.60e-06 |protein_coding | #> |ENSG00000000457 |SCYL3 |81 |-1.94 |2.77e-05 |protein_coding |