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