atacRepsPipe2: Pipeline for multi-replicates case-control paired-end...
In esATAC: An Easy-to-use Systematic pipeline for ATACseq data analysis

Description Usage Arguments Details Value Author(s) See Also Examples

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.

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,
  ...
)

`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.

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 ./)

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

Zheng Wei and Wei Zhang

atacPipe

## 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)