LncPath: Identifying the Pathways Regulated by LncRNA Sets of Interest

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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.

Author
Junwei Han, Zeguo Sun
Date of publication
2016-05-16 14:45:44
Maintainer
Junwei Han <hanjunwei1981@163.com>
License
GPL (>= 2)
Version
1.0

View on CRAN

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

Files in this package

LncPath
LncPath/inst
LncPath/inst/doc
LncPath/inst/doc/LncPath.R
LncPath/inst/doc/LncPath.pdf
LncPath/inst/doc/LncPath.Rnw
LncPath/NAMESPACE
LncPath/data
LncPath/data/datalist
LncPath/data/LncPathEnvir.rda
LncPath/R
LncPath/R/inner.r
LncPath/R/getExampleData.r
LncPath/R/findSigGenes.r
LncPath/R/lncPath.r
LncPath/R/getNet.r
LncPath/R/resultHandling.r
LncPath/vignettes
LncPath/vignettes/LncPath.Rnw
LncPath/MD5
LncPath/build
LncPath/build/vignette.rds
LncPath/DESCRIPTION
LncPath/man
LncPath/man/drawAHeatMap.Rd
LncPath/man/getExampleData.Rd
LncPath/man/printSignifResult.Rd
LncPath/man/getNet.Rd
LncPath/man/LncPathEnvir.Rd
LncPath/man/geneSetDetail.Rd
LncPath/man/lncPath.Rd
LncPath/man/LncPath-internal.Rd
LncPath/man/plotRunningES.Rd
LncPath/man/findSigGenes.Rd
LncPath/man/lncPath2Table.Rd