Elementolab/ChIPseeqerGetPCGenes

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	The following options are available:		The following options are available:
-	-projFile FILE This file is created from the ChIPseeqerModel script and contains the PC scores for all transcripts.	+	--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.	+	--pcNum INT Set this option to a number to specify the number of principal components you are going to extract the transcripts for.
		+	--thres NUMBER Set this threshold value to extract genes that have value > threshold
	Example of the '''projFile'''.		Example of the '''projFile'''.
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	...		...
	NM_001130845 0.0002		NM_001130845 0.0002
-	...
-	NM_001134738 -0.7238
-	NM_001006109 -1.3473
	'''IMPORTANT''': The scores are sorted numerically (from positive to negative values)		'''IMPORTANT''': The scores are sorted numerically (from positive to negative values)

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ChIPseeqerGetPCGenes

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:

ChIPseeqerGetPCGenes --projFile=MatPromBind.txt.proj

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.
--thres NUMBER          Set this threshold value to extract genes that have value > threshold

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

IMPORTANT: The scores are sorted numerically (from positive to negative values)