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.
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 <lg390@cam.ac.uk>
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")