# Pipeline framework for bioinformatics in R

## Documentation for package ‘pipeFrame’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

$ | 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