chicWrapper: ChIC analysis in one command

In carmencita/ChIC: Quality Control Pipeline for ChIP-Seq Data

Description

This function creates a single document (in pdf format) containing all the analysis plots produced by ChIC: the CrossCorrelation profile of the immunoprecipitation, the fingerprint plot and the different metagene profiles and returns the ChIC RF score.

chicWrapper

Usage

chicWrapper(
  chipName,
  inputName,
  read_length,
  savePlotPath = getwd(),
  target,
  annotationID,
  mc = 1,
  debug = FALSE
)

Arguments

chipName	String, filename and path to the ChIP bam file (without ".bam" extension)
inputName	String, filename and path to the Input bam file (without ".bam" extension)
read_length	Integer, length of the sequencing reads
savePlotPath	path, needs to be set to save the summary plot under "savePlotPath" (default=getwd()). In the current version of the code we MUST save the output summary plots in a PDF file. If the end users really needs to suppress the PDF output, they can use the "/dev/null" as output savePlotPath
target	String, chromatin mark or transcription factor to be analysed. Using the function "listAvailableElements" with the keywords "mark" and "TF" shows a list with the available elements.
annotationID	String, indicating the genome assembly
mc	Integer, the number of CPUs for parallelization (default=1)
debug	Boolean, to enter debugging mode. Intermediate files are saved in working directory

Value

ChIC RF score, returns the rnadom forest prediction score of the predictionScore() function, produces the summary report and saves it under "savePlotPath".

Examples

## This command is time intensive to run

## To run this example code the user MUST provide 2 bam files: one for 
## ChIP and one for the input. Here we used ChIP-seq data from ENCODE. 
## Two example files can be downloaded using the following link:
## https://www.encodeproject.org/files/ENCFF000BFX/
## https://www.encodeproject.org/files/ENCFF000BDQ/
## and save them in the working directory (here given in the temporary 
## directory "filepath"

mc=5
## Not run: 

filepath=tempdir()
setwd(filepath)

target= "H3K4me3"
system("wget 
https://www.encodeproject.org/files/ENCFF000BFX/@download/ENCFF000BFX.bam")
system("wget 
https://www.encodeproject.org/files/ENCFF000BDQ/@download/ENCFF000BDQ.bam")

chipName=file.path(filepath,"ENCFF000BFX")
inputName=file.path(filepath,"ENCFF000BDQ")

prediction=chicWrapper(chipName=chipName, inputName=inputName, 
target= "H3K4me3", read_length=36, mc=mc , savePlotPath=filepath)
print(prediction)

## End(Not run)

carmencita/ChIC documentation built on April 28, 2021, 7:20 p.m.