Learn R Programming

mGSZ (version 1.0)

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

Description

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.

Copy Link

Version

Install

install.packages('mGSZ')

Monthly Downloads

9

Version

1.0

License

GPL (>= 2)

Maintainer

Pashupati Mishra

Last Published

February 19th, 2014

Functions in mGSZ (1.0)

WRS.p.values

Internal WRS function
SS.p.values

Internal mGSZ function
mGSZ.test.score.stb3

Internal mGSZ function
mGSZ.test.score.stb4

Internal mGSZ function
StabPlotData

GSZ scoring function profile data
emp

Internal mGSZ function
KS.score

Internal KS function
KS.p.values

Internal KS function
FC

Internal mGSZ function
SS.test.score

Internal mGSZ function
mGSZ

Gene set analysis based on Gene Set Z-scoring function and asymptotic p-value
count.prob.sum

Internal mGSZ function
listTOclMatrix

Internal mGSZ function
logNORMcdf

Internal mGSZ function
mGSZ.adj.mean.std

Internal mGSZ function
mGSZ.test.score4

Internal mGSZ function
flipListStruct

Internal mGSZ function
pick.data.cols

Internal mGSZ function
diffScore

Internal mGSZ function
count_hyge_var_mean

Internal mGSZ function
sumVarMean_calc

Internal mGSZ function
mGSZ.p.values

Internal mGSZ function
mGSA.p.values

Internal mGSZ function
toTable

Table with top gene sets
plotProfile

Plot GSZ scoring function profile
toMatrix

Internal mGSZ function
mGSZ.test.score

Internal mGSZ function
mAllez.p.values

Internal mGSZ function
WRS.test.score

Internal WRS function
calc_z_var

Internal mGSZ function
rm.rows.with.noSetMembers

Internal mGSZ function
diffFCscore

Internal mGSZ function
geneSetsList

Convert gene set data in gmt file to R list
emp.wrs

Internal WRS function
logEVcdf

Internal mGSZ function
rm.small.genesets

Internal mGSZ function
mGSZ.test.score2

Internal mGSZ function
mGSZ.test.score.stb2

Internal mGSZ function
sumTestscore

Internal mGSZ function