Pipeline framework for bioinformatics in R

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Documentation for package ‘pipeFrame’ version 1.24.0

• 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