SCRenamer: Rename reads name in fastq

SCRenamerR Documentation

Rename reads name in fastq

Description

Rename reads name in fastq with increasing integer

Usage

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

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

scRenamer(
  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)


wzthu/ATACpipe documentation built on Aug. 12, 2022, 7:38 a.m.