atacRepsPipe {esATAC} | R Documentation |
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, motifPWM = NULL, prefix = NULL, chr = c(1:22, "X", "Y"), min.score = "90%", use.SavedPWM = NULL, ...)
genome |
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fastqInput1 |
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fastqInput2 |
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refdir |
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tmpdir |
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threads |
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adapter1 |
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adapter2 |
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interleave |
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createReport |
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motifPWM |
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prefix |
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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. |
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 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)