Top Tables of Differential Expression Results

Top Tables of Differential Expression Results

topTables(object, ...)

# S4 method for list
topTables(object, n = 50, coding = FALSE)

Arguments

object	DESeq2 results tables list generated by resultsTables().
...	Additional arguments (for the S4 generic definition).
n	Number genes to report.
coding	Whether to only return coding genes.

Value

Top table kables, for knit report.

Examples

resTbl <- resultsTables(res, write = FALSE)
#> Loading Ensembl annotations from AnnotationHub
#> 2017-10-27
#> EnsDB AH57770: Mus musculus Ensembl 90
#> 
#> 
#> ### Summary statistics
#> 
#> 
#> - 505 genes in count matrix
#> - base mean > 0: 304 genes (non-zero)
#> - base mean > 1: 213 genes
#> - alpha cutoff: 0.1
#> - lfc cutoff: 0 (applied in tables only)
#> - deg pass alpha: 4 genes
#> - deg lfc up: 2 genes
#> - deg lfc down: 2 genes
#> 
topTables(resTbl)
#> 
#> 
#> |ensgene            | baseMean|lfc   |padj    |symbol  |description           |
#> |:------------------|--------:|:-----|:-------|:-------|:---------------------|
#> |ENSMUSG00000104523 |      409|0.815 |7.7e-02 |Gm37335 |predicted gene, 37335 |
#> |ENSMUSG00000070960 |       15|7.307 |9.6e-02 |Gm19680 |predicted gene, 19680 |
#> 
#> 
#> |ensgene            | baseMean|lfc    |padj    |symbol |description          |
#> |:------------------|--------:|:------|:-------|:------|:--------------------|
#> |ENSMUSG00000016918 |      521|-0.992 |9.6e-02 |Sulf1  |sulfatase 1          |
#> |ENSMUSG00000048874 |     2484|-0.855 |9.6e-02 |Phf3   |PHD finger protein 3 |