PAGI: The package can identify the dysregulated KEGG pathways based on global influence from the internal effect of pathways and crosstalk between pathways.

The package can identify the dysregulated KEGG pathways based on global influence from the internal effect of pathways and crosstalk between pathways. (1) The PAGI package can prioritize the pathways associated with two biological states by statistical significance or FDR. (2) The PAGI package can evaluated the global influence factor (GIF) score in the global gene-gene network constructed based on the relationships of genes extracted from each pathway in KEGG database and the overlapped genes between pathways.

Install the latest version of this package by entering the following in R:
install.packages("PAGI")
AuthorJunwei Han,Yanjun Xu,Haixiu Yang,Chunquan Li and Xia Li
Bioconductor views Graphs Networks Pathways Statistics crosstalk
Date of publication2013-11-01 08:31:57
MaintainerJunwei Han <hanjunwei1981@163.com>
LicenseGPL (>= 2)
Version1.0

View on CRAN

Files

inst
inst/localdata
inst/localdata/dataset.txt
inst/localdata/class.labels.txt
inst/doc
inst/doc/PAGI.Rnw
inst/doc/PAGI.pdf
NAMESPACE
data
data/ExampleData.rda
data/datalist
data/PAGIData.rda
R
R/getExample.R R/PAGI.1.0.R
vignettes
vignettes/PAGI.Rnw
MD5
DESCRIPTION
man
man/PAGI.Main.Rd man/PAGI-internal.Rd man/ExampleData.Rd man/CalGIF.Rd man/getdataset.Rd man/getclass.labels.Rd man/PAGIData.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.