Differential Expression Results Tables

Differential Expression Results Tables

resultsTables(object, ...)

# S4 method for DESeqResults
resultsTables(object, lfc = 0, write = TRUE,
  summary = TRUE, headerLevel = 3, dir = file.path("results",
  "differential_expression"), organism = NULL, quiet = FALSE)

Arguments

object	Object.
...	Additional arguments (for the S4 generic definition).
lfc	Log fold change ratio (base 2) cutoff. Does not apply to statistical hypothesis testing, only gene filtering in the results tables. See results() for additional information about using lfcThreshold and altHypothesis to set an alternative hypothesis based on expected fold changes.
write	Write CSV files to disk.
summary	Show summary statistics as a Markdown list.
headerLevel	Markdown header level.
dir	Directory path where to write files.
organism	Optional. Override automatic genome detection. By default the function matches the genome annotations based on the first Ensembl gene identifier row in the object. If a custom FASTA spike-in is provided, then this may need to be manually set.
quiet	If TRUE, suppress any status messages and/or progress bars.

Value

Results list.

Examples

data(res)
resTbl <- resultsTables(res, lfc = 0.25, 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: 0.25 (applied in tables only)
#> - deg pass alpha: 4 genes
#> - deg lfc up: 2 genes
#> - deg lfc down: 2 genes
#> 
class(resTbl)
#> [1] "list"
names(resTbl)
#>  [1] "contrast"       "alpha"          "lfc"            "all"           
#>  [5] "deg"            "degLFC"         "degLFCUp"       "degLFCDown"    
#>  [9] "allFile"        "degFile"        "degLFCUpFile"   "degLFCDownFile"