atacRepsPipe {esATAC} | R Documentation

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

### Description

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.

### Usage

    atacRepsPipe(genome, fastqInput1, fastqInput2 = NULL, refdir = NULL,
      tmpdir = NULL, threads = 2, adapter1 = NULL, adapter2 = NULL,
      interleave = FALSE, createReport = TRUE, motifPWM = NULL,
      prefix = NULL, chr = c(1:22, "X", "Y"), min.score = "90%",
      use.SavedPWM = NULL, ...)

### Arguments

`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.
`motifPWM` | `List` scalar. Motif PWM, a list.
`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").
`min.score` | The minimum score for counting a match. Can be given as a character string containing a percentage (default: "90 possible score or as a single number.
`use.SavedPWM` | use local motif position information. This data is download or generate by users. it must be a rds file and the information saved as GRanges. Once this parameter is used, parameters "motifPWM" will be set to NULL.
`...` | Additional arguments, currently unused.

### Value

`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.

### Author(s)

Zheng Wei and Wei Zhang

### See Also

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

### 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 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",
           motifPWM = getMotifPWM(motif.file = system.file("extdata", "CTCF.txt", package="esATAC"), is.PWM = FALSE))

    # call pipeline
    # for overall example(all human 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)

[Package esATAC version 1.0.23 Index]