Renamer {esATAC} | R Documentation

## Rename reads name in fastq

### Description

Rename reads name in fastq with increasing integer

### Usage

    atacRenamer(
      atacProc,
      fastqOutput1 = NULL,
      fastqOutput2 = NULL,
      fastqInput1 = NULL,
      fastqInput2 = NULL,
      interleave = FALSE,
      threads = getThreads(),
      ...
    )

    ## S4 method for signature 'ATACProc'
    atacRenamer(
      atacProc,
      fastqOutput1 = NULL,
      fastqOutput2 = NULL,
      fastqInput1 = NULL,
      fastqInput2 = NULL,
      interleave = FALSE,
      threads = getThreads(),
      ...
    )

    renamer(
      fastqInput1 = NULL,
      fastqInput2 = NULL,
      fastqOutput1 = NULL,
      fastqOutput2 = NULL,
      interleave = FALSE,
      threads = getThreads(),
      ...
    )

### Arguments

`atacProc` | `ATACProc-class` object scalar. It has to be the return value of upstream process: `atacUnzipAndMerge` `unzipAndMerge`
`fastqOutput1` | `Character` scalar. The output file path of renamed fastqInput1.
`fastqOutput2` | `Character` scalar. The output file path of renamed fastqInput2.
`fastqInput1` | `Character` scalar. For single-end sequencing, it contains sequence file paths. For paired-end sequencing, it can be file path with #1 mates paired with file path in file2 And it can also be interleaved file paths when argument interleave=`TRUE`
`fastqInput2` | `Character` scalar. It contains file path with #2 mates paired with file paths in fastqInput1 For single-end sequencing files and interleaved paired-end sequencing files(argument interleaved=`TRUE`), it must be `NULL`.
`interleave` | `Character` scalar. Set `TRUE` when files are interleaved paired-end sequencing data.
`threads` | `Integer` scalar. The threads will be created in this process. default: 1
`...` | Additional arguments, currently unused.

### Details

The parameter related to input and output file path will be automatically obtained from `ATACProc-class` object(`atacProc`) or generated based on known parameters if their values are default(e.g. `NULL`). Otherwise, the generated values will be overwrited. If you want to use this function independently, you can use `renamer` instead.

### Value

An invisible `ATACProc-class` object scalar for downstream analysis.

### Author(s)

Zheng Wei

### See Also

`atacUnzipAndMerge` `unzipAndMerge` `atacQCReport` `atacRemoveAdapter`

### Examples

    ignoreCheck() # warnning: run this for fast test only
    library(magrittr)
    td <- tempdir()
    setTmpDir(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

    dir(td)

[Package esATAC version 1.9.3 Index]