gplink操作指南Word文档格式.docx

1、The top left panel shows the files contained in the PLINK project folder. The bottom panel shows the LOG file from any one particular PLINK run.Setting the project foldersInitiatlly, one must set the local project folder. Optionally, if running gPLINK in remote mode （where the data and computation r

2、eside on a remote server）, we will also set the remote project folder as well.Hit the Browse button to select a local project folder. If running gPLINK in local mode, this will typically be the folder where the genotype and phenotype files already reside. If running in remote mode, this local folder

3、 can be an empty folder - it is just used to store temporary files.Here we set the local project folder. In this example we are running in remote mode, so this is just an empty folder, wgas1.Now we instruct gPLINK that we are running in remote mode, by checking the Link to a remote project box once

4、we have selected the local folder. gPLINK uses the SSH protocol to connect to any server that provides this service. Enter the hostname and your username here. You probably want to leave the port number set to the default, 22.Now enter your password for your account on the server.Now select the remo

5、te project folder: this dialog will appear that lists all the files and folders on the remote machine. Navigate to the folder which contains the genotype and phenotype data and then click Open. In this case we select the folder that also happens to be called wgas1 although, remember this is a differ

6、ent folder from the local one, on a different machine.This dialog will appear only once, at the start of each new project （although you can change options later）. The top two options tell gPLINK where the PLINK program resides （either locally or remotely, depending on whether you are running in loca

7、l or remote mode）. The PLINK prefix option is design to facilitate using PLINK with a cluster computing environment if it is available （ for example, prefacing all commands in bsub）. If you are unfamiliar with the option and/or do not have access to a cluster, you can ignore this option. The other o

8、ptions on this panel are optional. You can tell gPLINK to also use an alternate viewer/editor （for example, emacs or Excel or any other program that accepts plain text files as input） by selecting the executable under User specified editor The auto save/updater option controls how frequently gPLINK

9、will check the local/remote computer （depending on the local/remote nature of the project） for completed operations and regularly save the operation history. Turning this feature off is not recomended and remote projects with slow connections may wish to increase the timing to 60 second intervals. I

10、f you have downloaded Haploview, you can tell gPLINK where the Haploview JAR file is on your local machine. This will enable integration between gPLINK and Haploview for viewing files and data. The bottom option is an advanced optional feature, which allows you to pass extra command flags to Haplove

11、w （for example, -memory 2000 to set the amount of memory Haploview has available）.After clicking on Browse to specify where Haploview is （from the previous gPLINK configuration dialog） you will see this dialog. Navigate to where Haploview is on your system Note, typically your version of Haploview w

12、ill be called just Haploview.jarThis shows the completed configuration form. The most important two things are that gPLINK knows where PLINK （either remotely or locally） and Haploview （always locally） live. Next time you open this project, this step will be skipped and gPLINK will remember the setti

13、ngs.Our first gPLINK commandNow we have finished configuration, we are finally ready to start looking at the data. In this case, the remote project contains a binary fileset called example （i.e. the PLINK data files example.bed, example.bim and example.fam already exist in the remote folder）. We cou

14、ld equally use gPLINK with standard text PED and MAP files also. We will use the Validate filset option from the Summary statistics menu to obtain basic counts of individuals and SNPs （this is equivalent to running PLINK with no command line options other than bfileValidate fileset dialogSelecting t

15、he menu option brings up this dialog. Most dialogs for other analyses look similar to this: In the top panel we specify the data: either a binary or standard fileset. Here we see the example fileset listed. If other filesets were in the project, the combo box could be used to select one of them. Additionally, the individual files （BED, BIM and FAM） can be individually specified instead （i.e. if they do not share the same file root, or if they reside in a direc