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

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

Functions

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

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