Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: locfit
locfit 1.5-9.1 2013-03-22
Loading required package: lattice
Welcome to 'DESeq'. For improved performance, usability and
functionality, please consider migrating to 'DESeq2'.
> system.file
function (..., package = "base", lib.loc = NULL, mustWork = FALSE)
{
if (nargs() == 0L)
return(file.path(.Library, "base"))
if (length(package) != 1L)
stop("'package' must be of length 1")
packagePath <- find.package(package, lib.loc, quiet = TRUE)
ans <- if (length(packagePath)) {
FILES <- file.path(packagePath, ...)
present <- file.exists(FILES)
if (any(present))
FILES[present]
else ""
}
else ""
if (mustWork && identical(ans, ""))
stop("no file found")
ans
}
<bytecode: 0x000000001abf07e0>
<environment: namespace:base>
> datafile = system.file( "extdata/pasilla_gene_counts.tsv", package="pasilla" )
> datafile = system.file
> system.file
function (..., package = "base", lib.loc = NULL, mustWork = FALSE)
{
if (nargs() == 0L)
return(file.path(.Library, "base"))
if (length(package) != 1L)
stop("'package' must be of length 1")
packagePath <- find.package(package, lib.loc, quiet = TRUE)
ans <- if (length(packagePath)) {
FILES <- file.path(packagePath, ...)
present <- file.exists(FILES)
if (any(present))
FILES[present]
else ""
}
else ""
if (mustWork && identical(ans, ""))
stop("no file found")
ans
}
<bytecode: 0x000000001abf07e0>
<environment: namespace:base>
> datafile = system.file( "extdata/ datafile = system.file( "extdata/pasilla_gene_counts.tsv", package="pasilla" )
Error: unexpected symbol in "datafile = system.file( "extdata/ datafile = system.file( "extdata"
> datafile = system.file( "extdata/GSE54167_Non-normalized_data.txt", package="DESeq" )
>
>
> browseVignettes("DESeq")
starting httpd help server ... done
>
Just posting a bunch of code isn't likely to get people to try to answer your question. What exactly are you trying to do?