LncPath: Identifying the Pathways Regulated by LncRNA Sets of Interest
Version 1.0

Identifies pathways synergisticly regulated by the interested lncRNA(long non-coding RNA) sets based on a lncRNA-mRNA(messenger RNA) interaction network. 1) The lncRNA-mRNA interaction network was built from the protein-protein interactions and the lncRNA-mRNA co-expression relationships in 28 RNA-Seq data sets. 2) The interested lncRNAs can be mapped into networks as seed nodes and a random walk strategy will be performed to evaluate the rate of each coding genes influenced by the seed lncRNAs. 3) Pathways regulated by the lncRNA set will be evaluated by a weighted Kolmogorov-Smirnov statistic as an ES Score. 4) The p value and false discovery rate value will also be calculated through a permutation analysis. 5) The running score of each pathway can be plotted and the heat map of each pathway can also be plotted if an expression profile is provided. 6) The rank and scores of the gene list of each pathway can be printed.

Browse man pages Browse package API and functions Browse package files

AuthorJunwei Han, Zeguo Sun
Date of publication2016-05-16 14:45:44
MaintainerJunwei Han <hanjunwei1981@163.com>
LicenseGPL (>= 2)
Version1.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("LncPath")

Man pages

drawAHeatMap: Draw a heatmap for the genes of a pathway
findSigGenes: Find genes significantly differentially expressed between two...
geneSetDetail: Gain insight into the detail of the genes in a certain...
getExampleData: Get the example data
getNet: Get the background lncRNA-mRNA interaction network
lncPath: Identify pathways synergisticly regulated by lncRNA sets.
lncPath2Table: Simplify the lncPath object into table
LncPathEnvir: The variables in the environment variable 'LncPathEnvir' of...
LncPath-internal: LncPath internal functions
plotRunningES: Visualize the Kolmogorov-Smirnov running score of pathway
printSignifResult: Output the details of significant pathways

Functions

ESNorm Man page Source code
Getenvir Man page
LncPathEnvir Man page
RandomWalk2igraph Man page Source code
calFD Man page Source code
calT Man page Source code
drawAHeatMap Man page Source code
findSigGenes Man page Source code
geneSetDetail Man page Source code
getExampleData Man page Source code
getNet Man page Source code
initializeLncPathEnvir Man page Source code
lncPath Man page Source code
lncPath.EnrichmentScore Man page Source code
lncPath.EnrichmentScore2 Man page Source code
lncPath.HeatMapPlot Man page Source code
lncPath2Table Man page Source code
plotRunningES Man page Source code
printSignifResult Man page Source code
rw Man page Source code

Files

inst
inst/doc
inst/doc/LncPath.R
inst/doc/LncPath.pdf
inst/doc/LncPath.Rnw
NAMESPACE
data
data/datalist
data/LncPathEnvir.rda
R
R/inner.r
R/getExampleData.r
R/findSigGenes.r
R/lncPath.r
R/getNet.r
R/resultHandling.r
vignettes
vignettes/LncPath.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/drawAHeatMap.Rd
man/getExampleData.Rd
man/printSignifResult.Rd
man/getNet.Rd
man/LncPathEnvir.Rd
man/geneSetDetail.Rd
man/lncPath.Rd
man/LncPath-internal.Rd
man/plotRunningES.Rd
man/findSigGenes.Rd
man/lncPath2Table.Rd
LncPath documentation built on May 20, 2017, 3:56 a.m.