xRDataLoader | R Documentation |
xRDataLoader
is supposed to load the package built-in RData.
xRDataLoader(
RData = c(NA, "GWAS2EF", "GWAS_LD", "IlluminaHumanHT",
"IlluminaOmniExpress", "ig.DO",
"ig.EF", "ig.GOBP", "ig.GOCC", "ig.GOMF", "ig.HPCM", "ig.HPMA",
"ig.HPMI", "ig.HPPA",
"ig.MP", "org.Hs.eg", "org.Hs.egDGIdb", "org.Hs.egDO", "org.Hs.egGOBP",
"org.Hs.egGOCC", "org.Hs.egGOMF", "org.Hs.egHPCM", "org.Hs.egHPMA",
"org.Hs.egHPMI",
"org.Hs.egHPPA", "org.Hs.egMP", "org.Hs.egMsigdbC1",
"org.Hs.egMsigdbC2BIOCARTA",
"org.Hs.egMsigdbC2CGP", "org.Hs.egMsigdbC2CPall",
"org.Hs.egMsigdbC2CP",
"org.Hs.egMsigdbC2KEGG",
"org.Hs.egMsigdbC2REACTOME", "org.Hs.egMsigdbC3MIR",
"org.Hs.egMsigdbC3TFT", "org.Hs.egMsigdbC4CGN", "org.Hs.egMsigdbC4CM",
"org.Hs.egMsigdbC5BP", "org.Hs.egMsigdbC5CC", "org.Hs.egMsigdbC5MF",
"org.Hs.egMsigdbC6", "org.Hs.egMsigdbC7", "org.Hs.egMsigdbH",
"org.Hs.egPS",
"org.Hs.egSF", "org.Hs.egPfam", "org.Hs.string", "org.Hs.PCommons_DN",
"org.Hs.PCommons_UN"),
RData.customised = NULL,
verbose = TRUE,
RData.location = "http://galahad.well.ox.ac.uk/bigdata",
guid = NULL
)
RData |
which built-in RData to load. It can be one of "GWAS2EF", "GWAS_LD", "IlluminaHumanHT", "IlluminaOmniExpress", "ig.DO", "ig.EF", "ig.GOBP", "ig.GOCC", "ig.GOMF", "ig.HPCM", "ig.HPMA", "ig.HPMI", "ig.HPPA", "ig.MP", "org.Hs.eg", "org.Hs.egDGIdb", "org.Hs.egDO", "org.Hs.egGOBP", "org.Hs.egGOCC", "org.Hs.egGOMF", "org.Hs.egHPCM", "org.Hs.egHPMA", "org.Hs.egHPMI", "org.Hs.egHPPA", "org.Hs.egMP", "org.Hs.egMsigdbC1", "org.Hs.egMsigdbC2BIOCARTA", "org.Hs.egMsigdbC2CGP", "org.Hs.egMsigdbC2CPall", "org.Hs.egMsigdbC2CP", "org.Hs.egMsigdbC2KEGG", "org.Hs.egMsigdbC2REACTOME", "org.Hs.egMsigdbC3MIR", "org.Hs.egMsigdbC3TFT", "org.Hs.egMsigdbC4CGN", "org.Hs.egMsigdbC4CM", "org.Hs.egMsigdbC5BP", "org.Hs.egMsigdbC5CC", "org.Hs.egMsigdbC5MF", "org.Hs.egMsigdbC6", "org.Hs.egMsigdbC7", "org.Hs.egMsigdbH", "org.Hs.egPS", "org.Hs.egSF", "org.Hs.egPfam", "org.Hs.string", "org.Hs.PCommons_DN", "org.Hs.PCommons_UN", "org.Hs.egGTExV4", "org.Hs.egGTExV6" |
RData.customised |
a file name for RData-formatted file. By default, it is NULL. It is designed when the user wants to import customised RData that are not listed in the above argument 'RData'. However, this argument can be always used even for those RData that are listed in the argument 'RData' |
verbose |
logical to indicate whether the messages will be displayed in the screen. By default, it sets to TRUE for display |
RData.location |
the characters to tell the location of built-in
RData files. By default, it remotely locates at
http://galahad.well.ox.ac.uk/bigdata; the development version
locates at http://galahad.well.ox.ac.uk/bigdata. For the user
equipped with fast internet connection, this option can be just left as
default. But it is always advisable to download these files locally.
Especially when the user needs to run this function many times, there
is no need to ask the function to remotely download every time (also it
will unnecessarily increase the runtime). For examples, these files (as
a whole or part of them) can be first downloaded into your current
working directory, and then set this option as:
|
guid |
a valid (5-character) Global Unique IDentifier for an OSF project. For example, 'gskpn' (see 'https://osf.io/gskpn'). If a valid provided and the query matched, it has priority over the one specified via RData.location |
any use-specified variable that is given on the right side of the assigement sign '<-', which contains the loaded RData. If the data cannot be loaded, it returns NULL.
If there are no use-specified variable that is given on the right side
of the assigement sign '<-', then no RData will be loaded onto the
working environment. To enable 'guid', please also install a package
"osfr" via BiocManager::install("osfr",dependencies=TRUE)
.
xRDataLoader
RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
## Not run:
ImmunoBase <- xRDataLoader(RData.customised='ImmunoBase')
org.Hs.eg <- xRDataLoader(RData='org.Hs.eg')
ig.HPPA <- xRDataLoader(RData='ig.HPPA')
org.Hs.egHPPA <- xRDataLoader(RData='org.Hs.egHPPA')
org.Hs.egHPPA <- xRDataLoader(RData.customised='org.Hs.egHPPA')
org.Hs.egHPPA <- xRDataLoader(RData.customised='org.Hs.egHPPA')
# from OSF
org.Mm.egKEGG <- xRDataLoader(RData='org.Mm.egKEGG', guid='gskpn')
org.Mm.string_high <- xRDataLoader(RData='org.Mm.string_high',
guid='gskpn')
## End(Not run)