$ | Methods for Step objects |
$-method | Methods for Step objects |
$<- | Methods for Step objects |
$<--method | Methods for Step objects |
addEdges | Step graph management |
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 |
genReport | Methods for Step objects |
getAutoPath | Methods for Step objects |
getAutoPath-method | Methods for Step objects |
getBasenamePrefix | Functions for directory operations |
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 |
getObjsInPipe | Obtain all of objects in the specific pipeline |
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 |
getPipeName | Configure the pipe name for following steps. |
getPrevSteps | Step graph management |
getRef | Set the reference directory |
getRefDir | Set the reference directory |
getRefFiles | Set the reference directory |
getRefRc | Set the reference directory |
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 |
pipeName | Methods for Step objects |
pipeName-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. |
setPipeName | Configure the pipe 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 |
stepID | Methods for Step objects |
stepID-method | Methods for Step objects |
stepName | Methods for Step objects |
stepName-method | Methods for Step objects |
stepType | Methods for Step objects |
stepType-method | Methods for Step objects |
Utils | Functions for directory operations |
writeLog | Methods for Step objects |
writeLog-method | Methods for Step objects |