atacPipe2 {esATAC} | R Documentation

## Pipeline for single replicate case-control paired-end sequencing data

### Description

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

### Usage

    atacPipe2(
      genome,
      case = list(fastqInput1 = "paths/To/fastq1", fastqInput2 = "paths/To/fastq2", adapter1
        = NULL, adapter2 = NULL),
      control = list(fastqInput1 = "paths/To/fastq1", fastqInput2 = "paths/To/fastq2",
        adapter1 = NULL, adapter2 = 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.
`case` | `List` scalar. Input for case sample. `fastqInput1`, the path(s) of the mate 1 fastq file(s), is required. `fastqInput2`, the path(s) of the mate 2 fastq file(s), is required, when `interleave=FALSE`. `adapter1` and `adapter2` are optional.
`control` | `List` scalar. Input for control sample. `fastqInput1`, the path(s) of the mate 1 fastq file(s), is required. `fastqInput2`, the path(s) of the mate 2 fastq file(s), is required, when `interleave=FALSE`. `adapter1` and `adapter2` are optional.
`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 "wholesummary": a dataframe for quality control summary of case and control data Slot "caselist" and "ctrlist": Each of them is a list that save the result for case or control data. Slots of "caselist" and "ctrllist": Slot "filelist": the input file paths. Slot "wholesummary": a dataframe for quality control summary of case or control data Slot "atacProcs": `ATACProc-class` objects generated by each process in the pipeline. Slot "filtstat": a dataframe that summary the reads filted in each process.

### 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 and BATF3 will be processed)
    conclusion <-
       atacPipe2(
           # MODIFY: Change these paths to your own case files!
           # e.g. fastqInput1 = "your/own/data/path.fastq"
           case=list(fastqInput1 = system.file(package="esATAC", "extdata", "chr20_1.1.fq.gz"),
                    fastqInput2 = 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"
           control=list(fastqInput1 = system.file(package="esATAC", "extdata", "chr20_1.2.fq.bz2"),
                        fastqInput2 = 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 <-
       atacPipe2(
           # MODIFY: Change these paths to your own case files!
           # e.g. fastqInput1 = "your/own/data/path.fastq"
           case=list(fastqInput1 = system.file(package="esATAC", "extdata", "chr20_1.1.fq.gz"),
                    fastqInput2 = 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"
           control=list(fastqInput1 = system.file(package="esATAC", "extdata", "chr20_1.2.fq.bz2"),
                        fastqInput2 = 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 1.9.3 Index]