SCRemoveAdapter: Use AdapterRemoval to remove adapters

In wzthu/ATACpipe: An Easy-to-use Systematic pipeline for ATACseq data analysis

Use AdapterRemoval to remove adapters

Description

Use AdapterRemoval to remove adapters

Usage

atacSCRemoveAdapter(
  atacProc,
  adapter1 = NULL,
  adapter2 = NULL,
  fastqOutput1 = NULL,
  reportPrefix = NULL,
  fastqOutput2 = NULL,
  fastqInput1 = NULL,
  fastqInput2 = NULL,
  interleave = FALSE,
  threads = getThreads(),
  paramList = NULL,
  findParamList = NULL,
  ...
)

## S4 method for signature 'ATACProc'
atacSCRemoveAdapter(
  atacProc,
  adapter1 = NULL,
  adapter2 = NULL,
  fastqOutput1 = NULL,
  reportPrefix = NULL,
  fastqOutput2 = NULL,
  fastqInput1 = NULL,
  fastqInput2 = NULL,
  interleave = FALSE,
  threads = getThreads(),
  paramList = NULL,
  findParamList = NULL,
  ...
)

scRemoveAdapter(
  fastqInput1,
  fastqInput2,
  adapter1,
  adapter2,
  fastqOutput1 = NULL,
  reportPrefix = NULL,
  fastqOutput2 = NULL,
  interleave = FALSE,
  threads = getThreads(),
  paramList = NULL,
  findParamList = NULL,
  ...
)

Arguments

atacProc	ATACProc-class object scalar. It has to be the return value of upstream process: atacRenamer renamer atacUnzipAndMerge unzipAndMerge
adapter1	Character. It is an adapter sequence for file1. For single end data, it is requied.
adapter2	Character. It is an adapter sequence for file2.
fastqOutput1	Character. The trimmed mate1 reads output file path for fastqInput2. Defualt: basename.pair1.truncated (paired-end), basename.truncated (single-end), or basename.paired.truncated (interleaved)
reportPrefix	Character. The prefix of report files path. Default: generate from known parameters
fastqOutput2	Character. The trimmed mate2 reads output file path for fastqInput2. Default: BASENAME.pair2.truncated (only used in PE mode, but not if –interleaved-output is enabled)
fastqInput1	Character vector. For single-end sequencing, it contains sequence file paths. For paired-end sequencing, it can be file paths with #1 mates paired with file paths in fastqInput2 And it can also be interleaved file paths when argument interleaved=TRUE
fastqInput2	Character vector. It contains file paths 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	Logical. Set TRUE when files are interleaved paired-end sequencing data.
threads	Numeric. The max threads allowed to be used by this step. Default: getThreads()
paramList	Additional arguments to be passed on to the binaries for removing adapter. See below for details.
findParamList	Additional arguments to be passed on to the binaries for identifying adapter. See below for details.
...	Additional arguments, currently unused.

Details

The parameter related to input and output file path will be automatically obtained from ATACProc-class object 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 scRemoveAdapter instead. You can put all aditional arguments in one Character(e.g. "–threads 8") with white space splited just like command line, or put them in Character vector(e.g. c("–threads","8")). Note that some arguments( "–file1","–file2","–adapter1","–adapter2","–output1","–output2", "–basename","–interleaved","thread") to the paramList and findParamList are invalid if they are already handled as explicit function arguments. See the output of adapterremoval_usage() for details about available parameters.

Value

An invisible ATACProc-class object scalar for downstream analysis.

Author(s)

Zheng Wei

See Also

atacRenamer renamer atacUnzipAndMerge unzipAndMerge atacBowtie2Mapping

Examples

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 %>% atacFindAdapter %>% atacSCRemoveAdapter

dir(td)

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