/////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////// ROS-DET: Robust detector of switching mechanisms in gene expression /////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////// Tutorial /////////////////////////////////////////////////////////// Binary files of ROS-DET are available from "http://www.bic.kyoto-u.ac.jp/pathway/kayano/ros-det.htm". The followings are a point-by-point tutorial for running the binary file. A simple workflow is: 1. download the binary file for your platform. 2. prepare input files for expression and label. 3-1. put the input files in the directory which includes the binary file. 3-2. execute the binary file from a command line on your platform (in the directory of 3-1.). 4. confirm the result in the output file. ------------------------------------- ------------------------------------- 1. Download ------------------------------------- ------------------------------------- The first step is to obtain a working copy of the binary file of ROS-DET and of the sample data files. Linux (x86_64) and Mac (i386, PPC) users should download "rosdet_linux.tar.gz" and "rosdet_mac.dmg", respectively. Each of the compressed files includes a binary file (rosdet), sample files ("exp.txt", "label.txt", "out_sample.txt") and a readme file. In the sample data files, the result of the sample input ("exp.txt", "label.txt") was output in "out_sample.txt". These input files include synthetic data of expression values of 8 genes for 30 individuals. ------------------------------------- ------------------------------------- 2. Prepare data files ------------------------------------- ------------------------------------- Each of input files contains numerical data which are written as a matrix formulation delimited by white spaces or tabs: ------------------------------------------------------- data type size (#rows -- #columns) delimiters ------------------------------------------------------- expression #genes -- n white space / tab label 1 -- n white space / tab ------------------------------------------------------- Where n is the number of the individuals. Each label should be 0 or 1. Both white space and tab are available as delimiters of data. However, continuing spaces and continuing tabs are NOT ALLOWED. The followings are examples of the sample input. ----------------------------------------- data type size delimiters ----------------------------------------- expression 8 -- 30 tab label 1 -- 30 white space ----------------------------------------- Each value in the label file includes class labels (0 or 1). ------------------------------------- ------------------------------------- 3. How to run ------------------------------------- ------------------------------------- After installing a binary file of ROS-DET and also installing your data for expressions and labels in a working directory, the binary file is executed as follows. Note that the binary file and the data files should be in a common directory. ------------- Linux and Mac ------------- Please type the following command at a terminal window, >> ./rosdet -e exp.txt -l label.txt -o out.txt and enter a significant level (for example 0.001) and number of gene pairs to be output after the corresponding message, >> significant level for gene pairs to be selected: >> number of gene pairs to be output: The binary file first inputs the significant level, the number of gene pairs and data files, and assigns the output file with "out.txt". After that, ROS-DET will be performed though ranking the gene combinations by WCOR and pruning the combinations by ECOR. The result is output in "out.txt". Options -e,-l,-o specify input and output files. '-e' specifies a data file for expression values of genes "exp.txt". '-l' specifies a data file for labels "label.txt". '-o' specifies an output file "out.txt". These specifications are in no particular order. For example, "./rosdet -e exp.txt -o out.txt -l label.txt" is acceptable, but "./rosdet -l exp.txt -o label.txt -e out.txt" is NOT ACCEPTABLE. The following command is for a help of the usage. >> ./rosdet -h ------------------------------------- ------------------------------------- 4. Result ------------------------------------- ------------------------------------- The result will be printed in the output file. ------- example ------- Results of ROS-DET: ------------------------------------------------- significant level = 0.001786 number of gene pairs to be output = 100 (maximum) ------------------------------------------------- rank score(WCOR) log10(p-value(ECOR)) gene X gene Y r1 r2 weight c 1 1.18 -10.83 7 8 0.86 -0.90 0.67 2 0.14 -9.07 5 6 0.88 -0.80 0.08 3 0.14 -6.61 3 4 0.95 -0.23 0.12