Export data out of R and write to disk.

# S4 method for DESeqAnalysis
export(x, name = NULL, dir = ".",
  compress = FALSE, humanize = FALSE)

Arguments

x

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.

humanize

logical(1). Make the gene and sample names human readable.

  • Gene names require geneName column to be defined in rowData().

  • Sample names require sampleName column to be defined in colData().

Examples

data(deseq) ## DESeqAnalysis ==== export(deseq, dir = "example")
#> Exporting DESeqDataSet.
#> Exporting assays: counts, mu, H, cooks
#> Exported counts.csv.
#> Exported mu.csv.
#> Exported H.csv.
#> Exported cooks.csv.
#> Exported colData.csv.
#> Dropping non-atomic columns: #> entrezID
#> Exported rowData.csv.
#> Exported data to /Users/mike/git/DESeqAnalysis/docs/reference/example/deseq/data.
#> #> Exporting DESeqTransform.
#> Exporting assays: counts, mu, H, cooks
#> Exported counts.csv.
#> Exported mu.csv.
#> Exported H.csv.
#> Exported cooks.csv.
#> Exported colData.csv.
#> Dropping non-atomic columns: #> entrezID
#> Exported rowData.csv.
#> Exported transform to /Users/mike/git/DESeqAnalysis/docs/reference/example/deseq/transform.
#> #> Exporting results.
#> Exported condition_B_vs_A.csv.
#> #> Exporting lfcShrink.
#> Exported condition_B_vs_A.csv.
#> #> Exporting results tables.
#> DESeqResults: 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)