Revision as of 20:29, 4 November 2010
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This script extracts for each principal component the transcripts and their scores (after PCA).
How to run the script
To run the script directly from any folder, you need to add the $CHIPSEEQERDIR and $CHIPSEEQERDIR/SCRIPTS to your $PATH. Read How to set the CHIPSEEQERDIR variable.
1. To run the program, type the command:
The following options are available:
-projFile FILE This file is created from the ChIPseeqerModel script and contains the PC scores for all transcripts. -pcNum INT Set this option to a number to specify the number of principal components you are going to extract the transcripts for.
Example of the projFile.
GENE PC1 PC2 PC3 NM_018117 2.6802 1.0600 -0.0294 NM_001130845 13.8136 12.4116 -2.2314 NM_021107 4.3074 1.8483 1.4885
How do the results look like
The output of this script is one file for each PC, named MatPromBind.txt.proj.PC1.transcripts.txt and so on.
Here's what these files will contain.
NM_001706 17.0907 NM_001029835 14.2258 NM_001518 12.1606 ... NM_001130845 0.0002 ... NM_001134738 -0.7238 NM_001006109 -1.3473
IMPORTANT: The scres are sorted numerically (from positive to negative values)