Export data out of R and write to disk.

export(object, ...)

# S4 method for DESeqDataSet
export(object, name = NULL, dir = ".",
  compress = FALSE)

# S4 method for DESeqAnalysis
export(object, name = NULL, dir = ".",
  compress = FALSE, lfcShrink = TRUE)

Arguments

object

Object.

name

character(1). Name to use on disk. If NULL, will use the name of the object instead.

dir

character(1). Directory path.

compress

logical(1). Apply gzip compression to all files.

lfcShrink

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

...

Additional arguments.

Value

Invisibily return file paths, either as list or character.

Examples

data(deseq) ## DESeqAnalysis ==== export(deseq, dir = "example")
#> Exporting DESeqDataSet.
#> Exporting assays: counts, normalized
#> Exported counts.csv.
#> Exported normalized.csv.
#> Exported colData.csv.
#> Dropping non-atomic columns: entrezID
#> Exported rowData.csv.
#> Exported data to /Users/mike/git/packages/DESeqAnalysis/docs/reference/example/deseq/data.
#> Exporting DESeqTransform.
#> Exporting assays: assay
#> Exported assay.csv.
#> Exported colData.csv.
#> Dropping non-atomic columns: entrezID
#> Exported rowData.csv.
#> Exported transform to /Users/mike/git/packages/DESeqAnalysis/docs/reference/example/deseq/transform.
#> Exporting DESeqResults tables.
#> condition_B_vs_A (shrunken LFC)
#> Returning with the sample names unmodified.
#> Joining row annotations.
#> Joining size factor adjusted normalized counts.
#> 171 differentially expressed genes detected.
#> 84 upregulated genes detected.
#> 87 downregulated genes detected.
#> Exported all.csv.
#> Exported up.csv.
#> Exported down.csv.
#> Exported both.csv.
## Clean up. unlink("example", recursive = TRUE)