getExampleData: Get the environment data

In SubpathwayLNCE: Identify Signal Subpathways Competitively Regulated by LncRNAs Based on ceRNA Theory

Description

Get variables in current environment.

Usage

GetExampleData(exampleData)

Arguments

exampleData

A character string. It must be one of them, including "code", "compound", "g2", "gene", "gene2path", "gene2symbol", "GeneExp", "keggGene2gene", "lnc2Name", "lncBackground", "LncExp", "LncGenePairs", "mart", "nocode", "pp", "resultT" and "sub".

Details

The parameter exampleData is "code", which represents to obtain all human coding gene collected from Genecode.

The parameter K2riData is "compound", which represents to obtain all huamn compound.

The parameter K2riData is "g2", which represents to obtain undirect KEGG metabolic pathway graphs with genes as nodes.

The parameter K2riData is "gene", which represents to obtain interseted gene of example.

The parameter K2riData is "gene2symbol", which represents to obtain gene-symbol data.

The parameter K2riData is "gene2path", which represents to obtain gene-pathway data.

The parameter K2riData is "GeneExp", which represents to obtain gene expression profile of example.

The parameter K2riData is "keggGene2gene", which represents to obtain kegggene-gene data.

The parameter K2riData is "lnc2Name", which represents to obtain lncRNA Ensemble-Name data.

The parameter K2riData is "lncBackground", which represents to obtain background of lncRNA, gene or lncRNA-gene.

The parameter K2riData is "LncExp", which represents to obtain lncRNA expression profile of example.

The parameter K2riData is "LncGenePairs", which represents to obtain the cmepetitively regulated lncRNA-mRNA interactions.

The parameter K2riData is "mart", which represents to obtain gene ensemble-name-entrez data.

The parameter K2riData is "nocode", which represents to obtain all huaman lncRNA collected from Genecode.

The parameter K2riData is "resultT", which represents to obtain result of example.

The parameter K2riData is "sub", which represents to obtain subpahtway of example.

The parameter K2riData is "geneLnc", which represents to obtain user-interested genes and lncRNAs of example.

Author(s)

Xinrui Shi, Chunquan Li and Xia Li

Examples

## Not run: 


# obtain lncRNA expression profile #
LncExp <- GetExampleData(exampleData="LncExp")



## End(Not run)

Example output

Loading required package: igraph

Attaching package: ‘igraph’

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:igraph’:

    normalize, path, union

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min


Attaching package: ‘graph’

The following objects are masked from ‘package:igraph’:

    degree, edges, intersection


Attaching package: ‘RBGL’

The following objects are masked from ‘package:igraph’:

    bfs, dfs, transitivity

Loading required package: BiasedUrn

Attaching package: ‘SubpathwayLNCE’

The following object is masked from ‘package:graph’:

    initialize

The following object is masked from ‘package:methods’:

    initialize

SubpathwayLNCE documentation built on May 1, 2019, 10:25 p.m.