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

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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.

Author
Junwei Han,Yanjun Xu,Haixiu Yang,Chunquan Li and Xia Li
Date of publication
2013-11-01 08:31:57
Maintainer
Junwei Han <hanjunwei1981@163.com>
License
GPL (>= 2)
Version
1.0

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Man pages

CalGIF
Calculate the global influence factor (GIF)
ExampleData
The variables in the environment variable ExampleData of the...
getclass.labels
Get the labels of example dataset
getdataset
Get the example dataset
PAGIData
The variables in the environment variable PAGIData of the...
PAGI-internal
PAGI internal functions
PAGI.Main
A novel pathway identification approach based on global...

Files in this package

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