/********************************************************************************/
/* FILENAME: samplepls.txt                                                      */
/*                                                                              */
/* DATE/LAST MODIFIED: 03.05.02/03.05.02/02.14.08                               */
/*                                                                              */
/* AUTHOR: Danh V. Nguyen, Biostatistics, UC Davis.                             */
/*                                                                              */
/* DESCRIPTION:                                                                 */
/* This file contains some sample SAS codes to run partial least squares (PLS). */
/* The codes below                                                              */
/*      1. read in a matrix of gene expression values of size nxp (here p=3846) */
/*         and a vector of class indicator (0 or 1) and                         */
/*      2. run PROC PLS.                                                        */
/* The expression matrix here is SPACE delimited. If your expression matrix is  */
/* TAB delimited (or another type), change the the line: delimiter=' ' (space)  */
/* to delimitor='	' (tab), etc.                                           */
/*                                                                              */
/* NOTES:                                                                       */
/* Comments can be found below along with the codes. For details on PLS see     */
/* the SAS documentation for PROC PLS (pp.2691-2734), SAS/STAT User's Guide,    */
/* Version 8, NC, SAS Institute Inc. (1999).  Many examples are given there.    */
/*                                                                              */
/* OUTPUT:                                                                      */
/* The data set OUTPLS includes the variables xscr1-xscr&lv, which are the PLS  */
/* gene components. You can run your favorite classification routine in SAS,    */
/* such as PROC LOGISTIC or PROC DISCRIM, or you can save the PLS gene          */
/* components and input it into your favorite program.                          */
/*                                                                              */
/* Have fun. Cheers. Danh                                                       */
/********************************************************************************/

options ls=80 ps=60;

/*------------------------------------------------------------------------------*/
/* Change these input parameters to suit your data set. 			*/
/*------------------------------------------------------------------------------*/
%let p=3051;
%let Xfilename=Xcomplete.txt;
%let Yfilename=Ycomplete.txt;


/* Load complete gene expression matrix, X. */
data Xcomp;
  infile "&Xfilename"
  delimiter=' ' lrecl=200000;
  input x1-x&p; run; 

/* Load response vector (matrix), Y. */
data Ycomp;
  infile "&Yfilename"
  delimiter=' ' lrecl=20000;
  input y; run;

data comb; merge Xcomp Ycomp; run;


%macro RUNPLS(dsxin, dsyin, p, lv);
proc pls data=&dsxin method=pls outmodel=EST1 lv=&lv;
  model &dsyin = x1-x&p;
  output out=OUTPLS p=yhat1 yresidual=yres1
  xresidual=xres1-xres&p
  xscore=xscr yscore=yscr
  stdy=stdy stdx=stdx h=h
  press=press t2=t2
  xqres=xqres yqres=yqres; run;
%mend;

	
/* The input lv is the number of PLS components, which should be specified. */
%RUNPLS(dsxin=comb, dsyin=y, p=3051, lv=2); /* lv=2 PLS components */
%RUNPLS(dsxin=comb, dsyin=y, p=3051, lv=5); /* lv=5 PLS components */