Installation¶
Download and Install:
Step1: Click on Get PCAtag on the left pane of the home page to download PCAtag.zip Step2: unzip PCAtag.zip to your local directory Step3: Click here to download sample files
Running PCAtag:
Start PCAtag in GUI mode:
- Double click on the jar file (PCAtag.jar)
Start PCAtag from the command prompt:
Step1: From the command prompt go to the directory where you extracted PCAtag.zip Step2: type “java -jar PCAtag.jar”
From the Command Line, the following command line parameters are supported:
��i�
��o�
��g� for genotype, default is �haplotype�
�-s� for subset analysis (separate analyses for each subset), default is �no subset analysis� (one analysis that considers all the data)
�-e� <Eigenvalue threshold [0.0..1.0]>, default is � 0.7�
�-v� <variance explained [0..100%]>, default value is �90%�
��f � <factor loading threshold for group membership [0.0-1.0]>� , default value is � 0.4�
�-t� < suppression for printing [0.0-1.0]> threshold below which the factor loading is not printed in the output, default value is � 0.2�
�-p� <short | long> short or long output print mode, default is �short�
short = Table 4 only
long = Tables 1, 2 , 3 and 4
� -2� for two step PCA analysis option, default multi-step
Example of appropriate syntax:
java -jar PCAtag.jar -i “C:\PCAtag\Input.txt” -o “C:\PCAtag\Output.txt”
System Requirements:
- 1 Gb free disk space
- Java 1.8 or newer