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

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.

AuthorPashupati Mishra, Petri Toronen
Date of publication2014-02-19 12:24:13
MaintainerPashupati Mishra <pashupati.mishra@helsinki.fi>
LicenseGPL (>= 2)
Version1.0

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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

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