xRDataLoader: Function to load the package built-in RData

In XGR: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis

Description

xRDataLoader is supposed to load the package built-in RData.

Usage

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 = T,
RData.location = "http://galahad.well.ox.ac.uk/bigdata",
guid = NULL
)

Arguments

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: RData.location=".". Surely, the location can be anywhere as long as the user provides the correct path pointing to (otherwise, the script will have to remotely download each time)
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

Value

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.

Note

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(c("remotes","centerforopenscience/osfr"),dependencies=T).

See Also

xRDataLoader

Examples

## 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)

XGR documentation built on Jan. 8, 2020, 5:06 p.m.