Pipeline framework for bioinformatics in R


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Documentation for package ‘pipeFrame’ version 1.0.0

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$ Methods for Step objects
$-method Methods for Step objects
addEdges Step graph management
argv Methods for Step objects
argv-method Methods for Step objects
argv<- Methods for Step objects
argv<--method Methods for Step objects
checkAllPath Methods for Step objects
checkAllPath-method Methods for Step objects
checkAndInstallBSgenome Install dependent data or software with finishing check
checkAndInstallGenomeFa Install dependent data or software with finishing check
checkAndInstallOrgDb Install dependent data or software with finishing check
checkAndInstallTxDb Install dependent data or software with finishing check
checkFileCreatable Functions for directory operations
checkFileExist Functions for directory operations
checkPathExist Functions for directory operations
checkRequireParam Methods for Step objects
checkRequireParam-method Methods for Step objects
clearStepCache Methods for Step objects
clearStepCache-method Methods for Step objects
getAutoPath Methods for Step objects
getAutoPath-method Methods for Step objects
getBasenamePrefix Functions for directory operations
getDefName Methods for Step objects
getDefName-method Methods for Step objects
getGenome Configure genome for all steps
getJobDir Configure the job name for following steps.
getJobName Configure the job name for following steps.
getNextSteps Step graph management
getParam Methods for Step objects
getParam-method Methods for Step objects
getParamItems Methods for Step objects
getParamItems-method Methods for Step objects
getParamMD5Path Methods for Step objects
getParamMD5Path-method Methods for Step objects
getPathPrefix Functions for directory operations
getPrevSteps Step graph management
getRef Set the reference directory
getRefDir Set the reference directory
getRefFiles Set the reference directory
getRefRc Set the reference directory
getReportItems Methods for Step objects
getReportItems-method Methods for Step objects
getReportItemsImp Methods for Step objects
getReportItemsImp-method Methods for Step objects
getReportVal Methods for Step objects
getReportVal-method Methods for Step objects
getReportValImp Methods for Step objects
getReportValImp-method Methods for Step objects
getStepId Methods for Step objects
getStepId-method Methods for Step objects
getStepName Methods for Step objects
getStepName-method Methods for Step objects
getStepWorkDir Methods for Step objects
getStepWorkDir-method Methods for Step objects
getThreads Configure the maximum number of threads
getTmpDir Configure the directory for intermediate results of all steps
getValidGenome Configure genome for all steps
graphMng Step graph management
init Methods for Step objects
init-method Methods for Step objects
initPipeFrame initialize the pipeFrame package
input Methods for Step objects
input-method Methods for Step objects
input<- Methods for Step objects
input<--method Methods for Step objects
isReady Methods for Step objects
isReady-method Methods for Step objects
output Methods for Step objects
output-method Methods for Step objects
output<- Methods for Step objects
output<--method Methods for Step objects
param Methods for Step objects
param-method Methods for Step objects
param<- Methods for Step objects
param<--method Methods for Step objects
printMap Step graph management
processing Methods for Step objects
property Methods for Step objects
property-method Methods for Step objects
property<- Methods for Step objects
property<--method Methods for Step objects
report Methods for Step objects
report-method Methods for Step objects
report<- Methods for Step objects
report<--method Methods for Step objects
runWithFinishCheck Install dependent data or software with finishing check
setGenome Configure genome for all steps
setJobName Configure the job name for following steps.
setRefDir Set the reference directory
setThreads Configure the maximum number of threads
setTmpDir Configure the directory for intermediate results of all steps
Step Methods for Step objects
Step-class Methods for Step objects
Utils Functions for directory operations
writeLog Methods for Step objects
writeLog-method Methods for Step objects