readEset: Read eSet object from plain files

In bedapub/ribiosExpression: Expression Analysis with RibiosExpression

Read eSet object from plain files

Description

Read eSet object from plain files

Usage

readEset(
  exprs.file,
  fData.file,
  pData.file,
  exprs.file.format = c("gct", "tsv"),
  sep = "\t",
  header = TRUE,
  ...
)

Arguments

exprs.file	Character, file name where exprs data is written to
fData.file	Character, optional, file name where fData data is written to
pData.file	Character, optional, file name where pData data is written to
exprs.file.format	Character, write exprs data in either gct or tsv format
sep	Character, separator
header	Logical, whether a head line is present
...	Passed to readFKtable The function can read in eSet object saved by writeEset by parsing three plain text files: exprs.file, fData.file, and pData.file. Currently both tsv and gct formats are supported for expression file. See writeEset for limitations of these functions.

See Also

writeEset, readFKtable.

Examples

data(sample.ExpressionSet, package="Biobase")
fData(sample.ExpressionSet) <- data.frame(
 ProbeID=featureNames(sample.ExpressionSet),
 row.names=featureNames(sample.ExpressionSet))
exprs.file <- tempfile()
fData.file <- tempfile()
pData.file <- tempfile()
writeEset(sample.ExpressionSet, exprs.file, fData.file, pData.file,
exprs.file.format="gct")
testRead1 <- readEset(exprs.file, fData.file, pData.file, exprs.file.format="gct")
writeEset(sample.ExpressionSet, exprs.file, fData.file, pData.file,
exprs.file.format="tsv")
testRead2 <- readEset(exprs.file, fData.file, pData.file, exprs.file.format="tsv")

bedapub/ribiosExpression documentation built on Sept. 2, 2023, 4:37 a.m.