functionall {DBGSA}R Documentation

P values of distance-based gene set enrichment analysis

Description

Function which cooperates all the functions claimed before, by using this function and the input data, we may get the p-values directly instead of running the functions step by step

Usage

functionall(fd,num,setdis,Meth,resultname,original,randgenenum,randtime,randname,presult)

Arguments

fd

Character string represents the name of a connection of the file to load, each row contains three items, Class labels of gene function, gene name and gene expression profile, each column represents the information of a class labels of gene function

num

An integer indecating the number of the case group

setdis

A character string indicating which method to be used to compute the distances between case group and control groupp, avelinkdis or centdis is the choice to choose

Meth

A character string indicates which method to be used to compute the distances between genes, euclidean and Manhattan is available to choose

resultname

Character string which represents the name of the output file which contains the distances between different label

original

Another input matrix representing the gene expression profile

randgenenum

An integer indicating the number of gene to be permutated, the number of it has to be larger than the gene number that any gene function label has.

randtime

An integer represents the number of permutation

randname

Character string representing the name of the output file which contains the result of permutation

presult

Character string representing the name of the output file which contains the result of p values

Value

A text containing the p values

Author(s)

Li Jin, Huang Meilin

See Also

distable, randdis, valuep

Examples

## Not run: 
data(afExp)
##before running this funtion, we need to find out "b1.txt" data file, and put it into the R workspace.
functionall(system.file("data","b1.txt",package="DBGSA"),10,avelinkdis,"euclidean","distance",afExp,2000,10,"rand.txt","pvalue.txt")
  
## End(Not run)

[Package DBGSA version 1.2 Index]