atacRepsPipe: Pipeline for multi-replicates case paired-end sequencing data
In esATAC: An Easy-to-use Systematic pipeline for ATACseq data analysis

Description Usage Arguments Value Author(s) See Also Examples

The preset pipeline to process multi-replicates case study sequencing data. HTML report files, result files(e.g. BED, BAM files) and conclusion list will generated. See detail for usage.

atacRepsPipe(
  genome,
  fastqInput1,
  fastqInput2 = NULL,
  refdir = NULL,
  tmpdir = NULL,
  threads = 2,
  adapter1 = NULL,
  adapter2 = NULL,
  interleave = FALSE,
  createReport = TRUE,
  motifs = NULL,
  prefix = NULL,
  chr = c(1:22, "X", "Y"),
  p.cutoff = 1e-06,
  ...
)

`genome`	`Character` scalar. The genome(like hg19, mm10, etc.) reference data in "refdir" to be used in the pipeline.
`fastqInput1`	`List` scalar. 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`. Each element in the fastqInput1 `List` is for a replicate It can be a `Character` vector of FASTQ files paths to be merged.
`fastqInput2`	`List` scalar. 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`. Each element in the fastqInput1 `List` is for a replicate It can be a `Character` vector of FASTQ files paths to be merged.
`refdir`	`Character` scalar. The path for reference data being installed to and storage.
`tmpdir`	`Character` scalar. The temporary file storage path.
`threads`	`Integer` scalar. The max threads allowed to be created.
`adapter1`	`Character` scalar. It is an adapter sequence for file1. For single end data, it is requied.
`adapter2`	`Character` scalar. It is an adapter sequence for file2.
`interleave`	`Logical` scalar. Set `TRUE` when files are interleaved paired-end sequencing data.
`createReport`	`Logical` scalar. If the HTML report file will be created.
`motifs`	either`PFMatrix`, `PFMatrixList`, `PWMatrix`, `PWMatrixList`, default: vertebrates motif from JASPAR.
`prefix`	`Character` scalar. Temporary file prefix for identifying files when multiple pipeline generating file in the same tempdir.
`chr`	Which chromatin the program will processing. It must be identical with the filename of cut site information files or subset of . Default:c(1:22, "X", "Y").
`p.cutoff`	p-value cutoff for returning motifs, default: 1e-6.
`...`	Additional arguments, currently unused.

List scalar. It is a list that save the result of the pipeline. Slot "filelist": the input file paths. Slot "wholesummary": a dataframe that for quality control summary Slot "atacProcs": ATACProc-class objects generated by each process in the pipeline. Slot "filtstat": a dataframe that summary the reads filted in each process.

Zheng Wei and Wei Zhang

printMap, atacPipe2, atacRenamer, atacRemoveAdapter, atacBowtie2Mapping, atacPeakCalling, atacMotifScan

## Not run: 
## These codes are time consuming so they will not be run and
## checked by bioconductor checker.


# call pipeline
# for a quick example(only CTCF and BATF3 will be processing)
conclusion <-
  atacRepsPipe(
       # MODIFY: Change these paths to your own case files!
       # e.g. fastqInput1 = "your/own/data/path.fastq"
       fastqInput1 = list(system.file(package="esATAC", "extdata", "chr20_1.1.fq.gz"),
                          system.file(package="esATAC", "extdata", "chr20_1.2.fq.bz2")),
       fastqInput2 = list(system.file(package="esATAC", "extdata", "chr20_2.1.fq.gz"),
                          system.file(package="esATAC", "extdata", "chr20_2.2.fq.bz2")),
       # MODIFY: Set the genome for your data
       genome = "hg19",
       motifs = getMotifInfo(motif.file = system.file("extdata", "CustomizedMotif.txt", package="esATAC")))

# call pipeline
# for overall example(all vertebrates motif in JASPAR will be processed)
conclusion <-
  atacRepsPipe(
       # MODIFY: Change these paths to your own case files!
       # e.g. fastqInput1 = "your/own/data/path.fastq"
       fastqInput1 = list(system.file(package="esATAC", "extdata", "chr20_1.1.fq.gz"),
                          system.file(package="esATAC", "extdata", "chr20_1.2.fq.bz2")),
       fastqInput2 = list(system.file(package="esATAC", "extdata", "chr20_2.1.fq.gz"),
                          system.file(package="esATAC", "extdata", "chr20_2.2.fq.bz2")),
       # MODIFY: Set the genome for your data
       genome = "hg19")

## End(Not run)