mGSZ: Gene set analysis based on GSZ-scoring function and asymptotic p-value
Version 1.0

Performs gene set analysis based on GSZ scoring function and asymptotic p-value. It is different from GSZ in that it implements asymptotic p-values instead of empirical p-values. Asymptotic p-values are calculated by fitting suitable distribution model to the null distribution. Unlike empirical p-values, resolution of asymptotic p-values are independent of the number of permutations and hence requires considerably fewer permutations. In addition, this package allows gene set analysis with seven other popular gene set analysis methods.

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AuthorPashupati Mishra, Petri Toronen
Date of publication2014-02-19 12:24:13
MaintainerPashupati Mishra <pashupati.mishra@helsinki.fi>
LicenseGPL (>= 2)
Version1.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("mGSZ")

Man pages

calc.z.var_int: Internal mGSZ function
count.hyge.var.mean_int: Internal mGSZ function
count.prob.sum_int: Internal mGSZ function
diffFCscore_int: Internal mGSZ function
diffScore_int: Internal mGSZ function
emp_int: Internal mGSZ function
emp.wrs_int: Internal WRS function
FC_int: Internal mGSZ function
flipListStruct_int: Internal mGSZ function
geneSetsList: Convert gene set data in gmt file to R list
KS.p.values_int: Internal KS function
KS.score_int: Internal KS function
listTOclMatrix_int: Internal mGSZ function
logEVcdf_int: Internal mGSZ function
logNORMcdf_int: Internal mGSZ function
mAllez.p.values_int: Internal mGSZ function
mGSA.p.values_int: Internal mGSZ function
mGSZ: Gene set analysis based on Gene Set Z-scoring function and...
mGSZ.adj.mean.std_int: Internal mGSZ function
mGSZ.p.values_int: Internal mGSZ function
mGSZ.test.score2_int: Internal mGSZ function
mGSZ.test.score4_int: Internal mGSZ function
mGSZ.test.score_int: Internal mGSZ function
mGSZ.test.score.stb2_int: Internal mGSZ function
mGSZ.test.score.stb3_int: Internal mGSZ function
mGSZ.test.score.stb4_int: Internal mGSZ function
pick.data.cols_int: Internal mGSZ function
plotProfile: Plot GSZ scoring function profile
rm.rows.with.noSetMembers_int: Internal mGSZ function
rm.small.genesets_int: Internal mGSZ function
SS.p.values_int: Internal mGSZ function
SS.test.score_int: Internal mGSZ function
StabPlotData: GSZ scoring function profile data
sumTestscore_int: Internal mGSZ function
sumVarMean.calc_int: Internal mGSZ function
toMatrix_int: Internal mGSZ function
toTable: Table with top gene sets
WRS.p.values_int: Internal WRS function
WRS.test.score_int: Internal WRS function

Functions

FC Man page Source code
KS.p.values Man page Source code
KS.score Man page Source code
SS.p.values Man page Source code
SS.test.score Man page Source code
StabPlotData Man page Source code
WRS.p.values Man page Source code
WRS.test.score Man page Source code
calc_z_var Man page Source code
count.prob.sum Man page Source code
count_hyge_var_mean Man page Source code
diffFCscore Man page Source code
diffScore Man page Source code
emp Man page Source code
emp.wrs Man page Source code
flipListStruct Man page Source code
geneSetsList Man page Source code Source code
listTOclMatrix Man page Source code
logEVcdf Man page Source code
logNORMcdf Man page Source code
mAllez.p.values Man page Source code
mGSA.p.values Man page Source code
mGSZ Man page Source code
mGSZ.adj.mean.std Man page Source code
mGSZ.p.values Man page Source code
mGSZ.test.score Man page Source code
mGSZ.test.score.stb2 Man page Source code
mGSZ.test.score.stb3 Man page Source code
mGSZ.test.score.stb4 Man page Source code
mGSZ.test.score2 Man page Source code
mGSZ.test.score4 Man page Source code
pick.data.cols Man page Source code
plotProfile Man page Source code
rm.rows.with.noSetMembers Man page Source code
rm.small.genesets Man page Source code
sumTestscore Man page Source code
sumVarMean_calc Man page Source code
toMatrix Man page Source code
toTable Man page Source code

Files

NAMESPACE
R
R/toMatrix.R
R/toTable.R
R/GSZ.R
R/StabPlotData.R
R/other.scores.R
R/geneSetsList.R
R/diffScore.R
R/pvals.R
R/mGSZ.R
R/plotProfile.R
MD5
DESCRIPTION
man
man/emp_int.Rd
man/logEVcdf_int.Rd
man/KS.p.values_int.Rd
man/emp.wrs_int.Rd
man/KS.score_int.Rd
man/toTable.Rd
man/sumTestscore_int.Rd
man/diffFCscore_int.Rd
man/count.prob.sum_int.Rd
man/plotProfile.Rd
man/sumVarMean.calc_int.Rd
man/pick.data.cols_int.Rd
man/mGSZ.test.score_int.Rd
man/geneSetsList.Rd
man/FC_int.Rd
man/toMatrix_int.Rd
man/mGSZ.test.score.stb4_int.Rd
man/flipListStruct_int.Rd
man/SS.p.values_int.Rd
man/mGSZ.test.score2_int.Rd
man/WRS.test.score_int.Rd
man/mGSZ.test.score.stb2_int.Rd
man/WRS.p.values_int.Rd
man/StabPlotData.Rd
man/listTOclMatrix_int.Rd
man/mGSZ.Rd
man/mGSZ.adj.mean.std_int.Rd
man/SS.test.score_int.Rd
man/mGSA.p.values_int.Rd
man/mGSZ.test.score.stb3_int.Rd
man/count.hyge.var.mean_int.Rd
man/rm.rows.with.noSetMembers_int.Rd
man/mGSZ.test.score4_int.Rd
man/rm.small.genesets_int.Rd
man/mGSZ.p.values_int.Rd
man/calc.z.var_int.Rd
man/diffScore_int.Rd
man/logNORMcdf_int.Rd
man/mAllez.p.values_int.Rd
mGSZ documentation built on May 19, 2017, 10:25 p.m.