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

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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.

Author
Pashupati Mishra, Petri Toronen
Date of publication
2014-02-19 12:24:13
Maintainer
Pashupati Mishra <pashupati.mishra@helsinki.fi>
License
GPL (>= 2)
Version
1.0

View on CRAN

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

Files in this package

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