gplink操作指南Word文档格式.docx
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ThetopleftpanelshowsthefilescontainedinthePLINKprojectfolder.
ThebottompanelshowstheLOGfilefromanyoneparticularPLINKrun.
Settingtheprojectfolders
Initiatlly,onemustsetthelocalprojectfolder.
Optionally,ifrunninggPLINKinremotemode(wherethedataandcomputationresideonaremoteserver),wewillalsosettheremoteprojectfolderaswell.
HittheBrowsebuttontoselectalocalprojectfolder.
IfrunninggPLINKinlocalmode,thiswilltypicallybethefolderwherethegenotypeandphenotypefilesalreadyreside.
Ifrunninginremotemode,thislocalfoldercanbeanemptyfolder--itisjustusedtostoretemporaryfiles.
Herewesetthelocalprojectfolder.
Inthisexamplewearerunninginremotemode,sothisisjustanemptyfolder,wgas1.
NowweinstructgPLINKthatwearerunninginremotemode,bycheckingtheLinktoaremoteprojectboxoncewehaveselectedthelocalfolder.gPLINKusestheSSHprotocoltoconnecttoanyserverthatprovidesthisservice.Enterthehostnameandyourusernamehere.Youprobablywanttoleavetheportnumbersettothedefault,22.
Nowenteryourpasswordforyouraccountontheserver.
Nowselecttheremoteprojectfolder:
thisdialogwillappearthatlistsallthefilesandfoldersontheremotemachine.
NavigatetothefolderwhichcontainsthegenotypeandphenotypedataandthenclickOpen.
Inthiscaseweselectthefolderthatalsohappenstobecalledwgas1although,rememberthisisadifferentfolderfromthelocalone,onadifferentmachine.
Thisdialogwillappearonlyonce,atthestartofeachnewproject(althoughyoucanchangeoptionslater).
ThetoptwooptionstellgPLINKwherethePLINKprogramresides(eitherlocallyorremotely,dependingonwhetheryouarerunninginlocalorremotemode).
ThePLINKprefixoptionisdesigntofacilitateusingPLINKwithaclustercomputingenvironmentifitisavailable(forexample,prefacingallcommandsinbsub).Ifyouareunfamiliarwiththeoptionand/ordonothaveaccesstoacluster,youcanignorethisoption.
Theotheroptionsonthispanelareoptional.YoucantellgPLINKtoalsouseanalternateviewer/editor(forexample,emacsorExceloranyotherprogramthatacceptsplaintextfilesasinput)byselectingtheexecutableunderUserspecifiededitor
The"
autosave/updater"
optioncontrolshowfrequentlygPLINKwillcheckthelocal/remotecomputer(dependingonthelocal/remotenatureoftheproject)forcompletedoperationsandregularlysavetheoperationhistory.Turningthisfeatureoffisnotrecomendedandremoteprojectswithslowconnectionsmaywishtoincreasethetimingto60secondintervals.
IfyouhavedownloadedHaploview,youcantellgPLINKwheretheHaploviewJARfileisonyourlocalmachine.ThiswillenableintegrationbetweengPLINKandHaploviewforviewingfilesanddata.
Thebottomoptionisanadvancedoptionalfeature,whichallowsyoutopassextracommandflagstoHaplovew(forexample,-memory2000tosettheamountofmemoryHaploviewhasavailable).
AfterclickingonBrowsetospecifywhereHaploviewis(fromthepreviousgPLINKconfigurationdialog)youwillseethisdialog.NavigatetowhereHaploviewisonyoursystem
Note,typicallyyourversionofHaploviewwillbecalledjustHaploview.jar
Thisshowsthecompletedconfigurationform.
ThemostimportanttwothingsarethatgPLINKknowswherePLINK(eitherremotelyorlocally)andHaploview(alwayslocally)live.
Nexttimeyouopenthisproject,thisstepwillbeskippedandgPLINKwillrememberthesettings.
OurfirstgPLINKcommand
Nowwehavefinishedconfiguration,wearefinallyreadytostartlookingatthedata.
Inthiscase,theremoteprojectcontainsabinaryfilesetcalledexample(i.e.thePLINKdatafilesexample.bed,example.bimandexample.famalreadyexistintheremotefolder).WecouldequallyusegPLINKwithstandardtextPEDandMAPfilesalso.
WewillusetheValidatefilsetoptionfromtheSummarystatisticsmenutoobtainbasiccountsofindividualsandSNPs(thisisequivalenttorunningPLINKwithnocommandlineoptionsotherthan–bfile
Validatefilesetdialog
Selectingthemenuoptionbringsupthisdialog.Mostdialogsforotheranalyseslooksimilartothis:
∙Inthetoppanelwespecifythedata:
eitherabinaryorstandardfileset.Hereweseetheexamplefilesetlisted.Ifotherfilesetswereintheproject,thecomboboxcouldbeusedtoselectoneofthem.Additionally,theindividualfiles(BED,BIMandFAM)canbeindividuallyspecifiedinstead(i.e.iftheydonotsharethesamefileroot,oriftheyresideinadirec