atacRepsPipe2 {esATAC} | R Documentation

## Pipeline for multi-replicates case-control paired-end sequencing data

### Description

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

### Usage

    atacRepsPipe2(
      genome,
      caseFastqInput1,
      caseFastqInput2,
      ctrlFastqInput1,
      ctrlFastqInput2,
      caseAdapter1 = NULL,
      caseAdapter2 = NULL,
      ctrlAdapter1 = NULL,
      ctrlAdapter2 = NULL,
      refdir = NULL,
      tmpdir = NULL,
      threads = 2,
      interleave = FALSE,
      createReport = TRUE,
      motifs = NULL,
      chr = c(1:22, "X", "Y"),
      p.cutoff = 1e-06,
      ...
    )

### Arguments

`genome` | `Character` scalar. The genome(like hg19, mm10, etc.) reference data in "refdir" to be used in the pipeline.
`caseFastqInput1` | `List` scalar. Input for case samples. 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 caseFastqInput1 `List` is for a replicate It can be a `Character` vector of FASTQ files paths to be merged.
`caseFastqInput2` | `List` scalar. Input for case samples. It contains file paths with #2 mates paired with file paths in caseFastqInput1 For single-end sequencing files and interleaved paired-end sequencing files(argument interleaved=`TRUE`), it must be `NULL`. Each element in the caseFastqInput2 `List` is for a replicate
`ctrlFastqInput1` | `List` scalar. Input for control samples. 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 ctrlFastqInput2 And it can also be interleaved file paths when argument interleaved=`TRUE`. Each element in the ctrlFastqInput1 `List` is for a replicate It can be a `Character` vector of FASTQ files paths to be merged.
`ctrlFastqInput2` | `List` scalar. Input for control samples. 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 ctrlFastqInput1 `List` is for a replicate
`caseAdapter1` | `Character` scalar. Adapter for caseFastqInput1.
`caseAdapter2` | `Character` scalar. Adapter for caseFastqInput2.
`ctrlAdapter1` | `Character` scalar. Adapter for ctrlFastqInput1.
`ctrlAdapter2` | `Character` scalar. Adapter for ctrlFastqInput2.
`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.
`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.
`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.

### Details

NOTE: Build bowtie index in this function may take some time. If you already have bowtie2 index files or you want to download(ftp://ftp.ccb.jhu.edu/pub/data/bowtie2_indexes) instead of building, you can let esATAC skip the steps by renaming them following the format (genome+suffix) and put them in reference installation path (refdir). Example: hg19 bowtie2 index files

- hg19.1.bt2

- hg19.2.bt2

- hg19.3.bt2

- hg19.4.bt2

- hg19.rev.1.bt2

- hg19.rev.2.bt2

For single end reads FASTQ files, The required parameters are fastqInput1 and adapter1. For paired end reads non-interleaved FASTQ files (interleave=FALSE,defualt), The required parameters are fastqInput1 and fastqInput2. Otherwise, parameter fastqInput2 is not required (interleave=TRUE)

The paths of sequencing data replicates can be a `Character` vector. For example:

fastqInput1=c("file_1.rep1.fastq","file_1.rep2.fastq")

fastqInput2=c("file_2.rep1.fastq","file_2.rep2.fastq")

The result will be return by the function. An HTML report file will be created for paired end reads. Intermediate files will be save at tmpdir path (default is ./)

### Value

`List` scalar. It is a list that save the result of the pipeline. Slot "caselist" and "ctrlist": Each of them is a list that save the result for case or control data. Slot "comp_result": compare analysis result for case and control data

### Author(s)

Zheng Wei and Wei Zhang

### See Also

`atacPipe`

### Examples

    ## 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 will be processed)
    conclusion <-
        atacRepsPipe2(
            # MODIFY: Change these paths to your own case files!
            # e.g. fastqInput1 = "your/own/data/path.fastq"
         caseFastqInput1=list(system.file(package="esATAC", "extdata", "chr20_1.1.fq.gz"),
                              system.file(package="esATAC", "extdata", "chr20_1.1.fq.gz")),
         # MODIFY: Change these paths to your own case files!
         # e.g. fastqInput1 = "your/own/data/path.fastq"
         caseFastqInput2=list(system.file(package="esATAC", "extdata", "chr20_2.1.fq.gz"),
                              system.file(package="esATAC", "extdata", "chr20_2.1.fq.gz")),
         # MODIFY: Change these paths to your own control files!
         # e.g. fastqInput1 = "your/own/data/path.fastq"
         ctrlFastqInput1=list(system.file(package="esATAC", "extdata", "chr20_1.2.fq.bz2"),
                              system.file(package="esATAC", "extdata", "chr20_1.2.fq.bz2")),
         # MODIFY: Change these paths to your own control files!
         # e.g. fastqInput1 = "your/own/data/path.fastq"
         ctrlFastqInput2=list(system.file(package="esATAC", "extdata", "chr20_2.2.fq.bz2"),
                              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 human motif in JASPAR will be processed)
    conclusion <-
        atacRepsPipe2(
            # MODIFY: Change these paths to your own case files!
            # e.g. fastqInput1 = "your/own/data/path.fastq"
         caseFastqInput1=list(system.file(package="esATAC", "extdata", "chr20_1.1.fq.gz"),
                              system.file(package="esATAC", "extdata", "chr20_1.1.fq.gz")),
         # MODIFY: Change these paths to your own case files!
         # e.g. fastqInput1 = "your/own/data/path.fastq"
         caseFastqInput2=list(system.file(package="esATAC", "extdata", "chr20_2.1.fq.gz"),
                              system.file(package="esATAC", "extdata", "chr20_2.1.fq.gz")),
         # MODIFY: Change these paths to your own control files!
         # e.g. fastqInput1 = "your/own/data/path.fastq"
         ctrlFastqInput1=list(system.file(package="esATAC", "extdata", "chr20_1.2.fq.bz2"),
                              system.file(package="esATAC", "extdata", "chr20_1.2.fq.bz2")),
         # MODIFY: Change these paths to your own control files!
         # e.g. fastqInput1 = "your/own/data/path.fastq"
         ctrlFastqInput2=list(system.file(package="esATAC", "extdata", "chr20_2.2.fq.bz2"),
                              system.file(package="esATAC", "extdata", "chr20_2.2.fq.bz2")),
         # MODIFY: Set the genome for your data
         genome = "hg19"
         )

    ## End(Not run)

[Package esATAC version 1.12.0 Index]