# dcoxss reference manual


1. dcoxs(x,y,gse1,gse2,method='pearson')

  1) input parameters 
     
     x,y; whole gene set expression matrix (p by n) of different conditions (A&B). gene names should be in the row names. 
     gse1,gse2; vectors containing gene names for each gene set. 
     method; mode for calculating correlation coefficient. 'spearman' & 'kendall' are also available. 

  2) output values

     The returned list object contains 7 elements.

     first element; interaction score (IS) of gse1 and gse2 in the condition A
     second element; p value of IS in the condition A 
     third element; IS of gse1 and gse2 in the condition B
     forth element; p value of IS in the condition B
     fifth element; difference of Fisher's Z transformed IS between the two conditions
     sixth element; p value of the difference
     seventh element; subset of gene set 1 & 2 containing no intersection members



2. dcoxs.plot((x,y,gse1,gse2,xlab,ylab,method='pearson')

  1) input parameters 

     xlab,ylab; gene set names
     The remaining parameters are the same with dcoxss function

  2) output 

     two IS plots in each condition

 
 
3. Usage

   1) re<-dcoxs(norm,ca,gse1,gse2,method='pearson)

      norm; gene expression matrix in the normal tissue
      ca; gene expression matrix in the cancer tissue

      gse1,gse2; gene name vectors of two different gene sets (for example, p53 pathway and wnt pathway)

      re[[1]],re[[2]]; IS and its p-value of gse1&2 in normal tissue
      re[[3]],re[[4]]; IS and its p-value of gse1&2 in cancer tissue
      re[[5]],re[[6]]; difference of IS and its p-value 
      re[[7]]; list containing two gene name vectors. they are subsets of two different gene sets containing no intersection gene members


   2) dcoxs.plot(norm,ca,re[[7]][[1]],re[[7]][[2]],'p53 pathway','wnt pathway',method='pearson')

      This function yields two plots of fitted line representing IS in each condition. 
    
      re[[7]][[1]],re[[7]][[2]]; The two vectors contain mutually independent gene names. 
      'p53 pathway', 'wnt pathway'; gene set names

      re is an object obtained from dcoxs function (See Usage 3-1)