PXDataset-class {rpx} | R Documentation |
"PXDataset"
An S4 class to store and access information about ProteomeXchange (PX) data sets. Schema versions 1.0, 1.1 and 1.2 are supported and are documented on the PX code repository: https://code.google.com/p/proteomexchange/source/browse/schema/
Objects can be created with the constructor PXDataset
.
id
:Object of class "character"
storing the
datasets unique identifier. Can be accessed with pxid()
.
formatVersion
:Object of class "character"
storing the version of the ProteomeXchange schema.
Data
:Object of class "XMLNode"
storing the
ProteomeXchange description as XML node tree.
signature(object = "PXDataset")
: return a
character
of all available files.
signature(object = "PXDataset", list, force =
FALSE, destdir = getwd(), ...)
: downloads the files from the
ProteomeXchange repository. If list
is missing, the file to
be downloaded can be selected from a menu. If list = "all"
,
all files are downloaded. The file names, as returned by
pxfiles
can also be used. Alternatively, a logical
or numeric
indices can be used. All files will be
downloaded into the directory specified by destdir
(default
is the current working directory). Unless force
is set to
TRUE
, files are not downloaded if already present in the
destdir
directory. Additional parameters can be passed to
download.file
via ...
. Invisibly returns the
names of the downloaded files.
On Windows, the error
In download.file(urls[i], toget[i], ...) : InternetOpenUrl failed: 'The login request was denied'
had been reported when downloading files. In such cases, the
method
argument to download.file
can be set. If
libcurl
is available (try capailities("libcurl")
to
check this), using pxget(..., method = "libcurl")
has
proven successful. See ?download.file
for more details.
signature(object = "PXDataset")
: returns the
unique ProteomeXchange identifier.
signature(object = "PXDataset")
: returns the
reference associcated with the object
.
signature(object = "PXDataset")
: returns the
scientic taxonomic name of object
.
signature(object = "PXDataset"
: returns the base
url on the ProteomeXchange server where pxfiles(object)
reside.
signature(object = "PXDataset")
: textual
representation of object
.
Laurent Gatto
Vizcaino J.A. et al. 'ProteomeXchange: globally co-ordinated proteomics data submission and dissemination', Nature Biotechnology 2014, 32, 223 – 226, doi:10.1038/nbt.2839.
Source repository for the ProteomeXchange project: https://code.google.com/p/proteomexchange/
px <- PXDataset("PXD000001") px pxtax(px) pxurl(px) pxref(px) pxfiles(px) fnm <- pxget(px, "PXD000001_mztab.txt") library("MSnbase") readMzTabData(fnm, "PEP") unlink("PXD000001_mztab.txt")