functionall: P values of distance-based gene set enrichment analysis
In DBGSA: methods of distance-based gene set functional enrichment analysis.

Description Usage Arguments Value Author(s) See Also Examples

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

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

`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

A text containing the p values

Li Jin, Huang Meilin

distable, randdis, valuep

## 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)