export | R Documentation |
Export
export(object, con, format, ...) ## S4 method for signature 'DESeqAnalysis,character,missingOrNULL' export( object, con, format, compress = getOption(x = "acid.export.compress", default = FALSE), overwrite = getOption(x = "acid.overwrite", default = TRUE), quiet = getOption(x = "acid.quiet", default = FALSE) ) ## S4 method for signature 'DESeqAnalysis,missingOrNULL,missingOrNULL' export(object, con, format, name = NULL, dir, ...) ## S4 method for signature 'DESeqDataSet,character,missingOrNULL' export( object, con, format, compress = getOption(x = "acid.export.compress", default = FALSE), overwrite = getOption(x = "acid.overwrite", default = TRUE), quiet = getOption(x = "acid.quiet", default = FALSE) ) ## S4 method for signature 'DESeqDataSet,missingOrNULL,missingOrNULL' export(object, con, format, name = NULL, dir, ...)
object |
Object.
An object supporting |
con |
|
format |
|
compress |
|
overwrite |
|
quiet |
|
name |
|
dir |
|
... |
Additional arguments. |
Size-factor normalized coutns and FPKM values are calculated on the fly and exported automatically.
Invisible character
.
File path(s).
matrix
supported arguments:
Comma separated values (CSV):
"csv"
, "csv.bz2"
, "csv.gz"
, "csv.xz"
, "csv.zip"
.
Tab separated values (TSV):
"tsv"
, "tsv.bz2"
, "tsv.gz"
, "tsv.xz"
, "tsv.zip"
.
Matrix
(sparseMatrix
) supported arguments:
MatrixMarket exchange (MTX):
"mtx"
, "mtx.bz2"
, "mtx.gz"
, "mtx.xz"
, "mtx.zip"
.
Some export utilities in R have a tendency to drop row names when writing to
disk in CSV format. For example, the readr family of functions never
write row names by design. This is a really poor default setting for
handling genomic data, which often contain gene identifiers in the row names.
Here we're performing any internal tibble coercion step to ensure row names
are always moved to a "rowname"
column in the CSV export.
Note that this function currently wraps readr::write_delim()
by default
for exporting DataFrame
, data.frame
, and matrix
class objects.
Updated 2022-05-17.
Packages:
rio.
Export functions:
BiocIO::export()
.
data.table::fwrite()
.
readr::write_delim()
.
rio::export()
.
rtracklayer::export()
.
vroom::vroom_write()
.
data(deseq) ## DESeqAnalysis ==== con <- AcidBase::tempdir2() x <- export(deseq, con = con) print(x) AcidBase::unlink2(con)
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