MetaPath: Perform the Meta-Analysis for Pathway Enrichment Analysis (MAPE)

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Perform the Meta-analysis for Pathway Enrichment (MAPE) methods introduced by Shen and Tseng (2010). It includes functions to automatically perform MAPE_G (integrating multiple studies at gene level), MAPE_P (integrating multiple studies at pathway level) and MAPE_I (a hybrid method integrating MAEP_G and MAPE_P methods). In the simulation and real data analyses in the paper, MAPE_G and MAPE_P have complementary advantages and detection power depending on the data structure. In general, the integrative form of MAPE_I is recommended to use. In the case that MAPE_G (or MAPE_P) detects almost none pathway, the integrative MAPE_I does not improve performance and MAPE_P (or MAPE_G) should be used. Reference: Shen, Kui, and George C Tseng. Meta-analysis for pathway enrichment analysis when combining multiple microarray studies.Bioinformatics (Oxford, England) 26, no. 10 (April 2010): 1316-1323. doi:10.1093/bioinformatics/btq148. http://www.ncbi.nlm.nih.gov/pubmed/20410053.

Author
Kui Shen and Geroge Tseng
Date of publication
2015-10-03 07:57:54
Maintainer
Kui Shen <kuishen@alumni.pitt.edu>
License
GPL (>= 2.0)
Version
1.0

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Man pages

cor.func
internal functions from Dr. Tibshirani's software package GSA
coxfunc
internal functions from Dr. Tibshirani's software package GSA
cox.perm.sample
internal functions from Dr. Tibshirani's software package GSA
coxscor
internal functions from Dr. Tibshirani's software package GSA
coxstuff
internal functions from Dr. Tibshirani's software package GSA
coxvar
internal functions from Dr. Tibshirani's software package GSA
Enrichment_KS_gene
internal functions
Enrichment_KS_sample
internal functions
F.perm.sample
internal functions
MAPE
perform the Meta-Analysis for Pathway Enrichment (MAPE)...
MAPE_G_gene_KS
internal functions
MAPE_G_sample_KS
internal functions
MAPE_I_KS
internal functions
MAPE_P_gene_KS
internal functions
MAPE_P_sample_KS
internal functions
MAQC
The data sets from MAQC project.
MetaPath-package
Perform the Meta-Analysis for Pathway Enrichment (MAPE)...
pathway.DB
An example of pathway database.
plotMAPE
Plot MAPE outcomes
pqvalues.compute
internal functions
reg.perm.sample
internal functions
Tperm.sample
internal functions

Files in this package

MetaPath
MetaPath/NAMESPACE
MetaPath/data
MetaPath/data/pathway.DB.rda
MetaPath/data/MAQC.rda
MetaPath/data/datalist
MetaPath/R
MetaPath/R/MAPE_G_gene_KS.R
MetaPath/R/F.perm.sample.R
MetaPath/R/Enrichment_KS_gene.R
MetaPath/R/plotMAPE.R
MetaPath/R/coxstuff.R
MetaPath/R/cor.func.R
MetaPath/R/coxvar.R
MetaPath/R/Enrichment_KS_sample.R
MetaPath/R/coxfunc.R
MetaPath/R/Tperm.sample.R
MetaPath/R/MAPE_I_KS.R
MetaPath/R/coxscor.R
MetaPath/R/reg.perm.sample.R
MetaPath/R/MAPE.R
MetaPath/R/MAPE_P_sample_KS.R
MetaPath/R/MAPE_G_sample_KS.R
MetaPath/R/MAPE_P_gene_KS.R
MetaPath/R/pqvalues.compute.R
MetaPath/R/cox.perm.sample.R
MetaPath/MD5
MetaPath/DESCRIPTION
MetaPath/man
MetaPath/man/cor.func.Rd
MetaPath/man/coxvar.Rd
MetaPath/man/MAQC.Rd
MetaPath/man/MAPE_G_sample_KS.Rd
MetaPath/man/coxfunc.Rd
MetaPath/man/Enrichment_KS_sample.Rd
MetaPath/man/Enrichment_KS_gene.Rd
MetaPath/man/plotMAPE.Rd
MetaPath/man/F.perm.sample.Rd
MetaPath/man/MAPE.Rd
MetaPath/man/pathway.DB.Rd
MetaPath/man/coxscor.Rd
MetaPath/man/MAPE_G_gene_KS.Rd
MetaPath/man/MAPE_P_sample_KS.Rd
MetaPath/man/MetaPath-package.Rd
MetaPath/man/MAPE_I_KS.Rd
MetaPath/man/coxstuff.Rd
MetaPath/man/pqvalues.compute.Rd
MetaPath/man/cox.perm.sample.Rd
MetaPath/man/Tperm.sample.Rd
MetaPath/man/reg.perm.sample.Rd
MetaPath/man/MAPE_P_gene_KS.Rd