ATACProc-class {esATAC} | R Documentation |
You can call ATACProc objects operation methods below to obtain information in objects.
## S4 method for signature 'ATACProc' atacPrintMap(atacProc, preProc = FALSE, nextProc = TRUE, curProc = TRUE, display = TRUE) printMap(atacProc = NULL, preProc = FALSE, nextProc = TRUE, curProc = TRUE, display = TRUE) ## S4 method for signature 'ATACProc' process(.Object, ...) ## S4 method for signature 'ATACProc' getProcName(.Object, ...) ## S4 method for signature 'ATACProc' getParam(.Object, item, ...) ## S4 method for signature 'ATACProc' getParamItems(.Object, ...) ## S4 method for signature 'ATACProc' isReady(.Object, ...) ## S4 method for signature 'ATACProc' clearProcCache(.Object, ...) ## S4 method for signature 'ATACProc' isSingleEnd(.Object, ...) ## S4 method for signature 'ATACProc' getReportVal(.Object, item, ...) ## S4 method for signature 'ATACProc' getReportItems(.Object, ...)
atacProc |
Character scalar. The ATACProc subclass name
for |
preProc |
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nextProc |
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curProc |
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display |
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.Object |
ATACProc object scalar. ATACProc object return by process functions. |
... |
Additional arguments, currently unused. |
item |
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ATACProc is a S4 class for generating ATACProc S4 objects. All ATACProc objects generated by its subclasses. You can only use the ATACProc objects returned by any functions rather than use ATACProc S4 class to generate object yourself.
the function and result of functions:
atacPrintMap |
Print map to locate the atacProc object in charflow |
printMap |
Print map to locate the atacProc name in charflow |
process |
Call this function to redo processing |
getProcName |
get ATACProc object Characher name |
getParam |
Get parameter value set by process function.
See |
getParamItems |
Get parameter name list |
isReady |
Is the process ready for downstream process |
clearProcCache |
Clear cache of atacProc object |
isSingleEnd |
Single end data if TRUE else FALSE |
getReportVal |
Get report value of item.
See |
getReportItems |
Get all items that can be reported |
Zheng Wei
library(magrittr) td <- tempdir() options(atacConf=setConfigure("tmpdir",td)) # Identify adapters prefix<-system.file(package="esATAC", "extdata", "uzmg") (reads_1 <-file.path(prefix,"m1",dir(file.path(prefix,"m1")))) (reads_2 <-file.path(prefix,"m2",dir(file.path(prefix,"m2")))) reads_merged_1 <- file.path(td,"reads1.fastq") reads_merged_2 <- file.path(td,"reads2.fastq") atacproc <- atacUnzipAndMerge(fastqInput1 = reads_1,fastqInput2 = reads_2) %>% atacRenamer %>% atacRemoveAdapter subclassname<-getProcName(atacproc) printMap(subclassname) (pitems<-getParamItems(atacproc)) getParam(atacproc,pitems[1]) isReady(atacproc) isSingleEnd(atacproc) (ritems<-getReportItems(atacproc)) getReportVal(atacproc,ritems[1]) clearProcCache(atacproc) process(atacproc)