# Pipeline framework for bioinformatics in R

## Documentation for package ‘pipeFrame’ version 1.4.0

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

## Help Pages

A C G I L O P R S U W misc

## -- A --

addEdges | Step graph management
addFileSuffix | Functions for directory operations
argv | Methods for Step objects
argv-method | Methods for Step objects

## -- C --

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
configRegName | load configure from file

## -- G --

genReport | Methods for Step objects
getAttachedStep | Step graph management
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

## -- I --

ignoreCheck | ignore checking input and output file (for developer)
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

## -- L --

loadConfig | load configure from file
loadStep | load step object from rds file

## -- O --

output | Methods for Step objects
output-method | Methods for Step objects
output<- | Methods for Step objects
output<--method | Methods for Step objects

## -- P --

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

## -- R --

regAttachedStep | Step graph management
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

## -- S --

saveConfig | load configure from file
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

## -- U --

Utils | Functions for directory operations

## -- W --

writeLog | Methods for Step objects
writeLog-method | Methods for Step objects

## -- misc --

$ | Methods for Step objects
$-method | Methods for Step objects
$<- | Methods for Step objects
$<--method | Methods for Step objects