generate_qc_report: Create a HTML QC report

In LiuzLab/TraceQC: Quality Control of CRISPR Lineage Tracing Seqence Data

Create a HTML QC report

Description

Create a HTML QC report

Usage

generate_qc_report(
  input_file = NULL,
  ref_file = NULL,
  fastqc_dir = NULL,
  output_path = NULL,
  ncores = 4,
  title = "TraceQC report",
  preview = FALSE
)

Arguments

input_file	A path of a FASTQ file.
ref_file	A path of a text file which contains construct information.
fastqc_dir	A directory path to store FastQC files. It will be omiited if it is set as NULL
output_path	A file path to save the HTML report. It will be omiited if it is set as NULL
ncores	The number of cores for parallel processing.
title	The title of the report.
preview	It will open a preview to a web-browser if the argument is set to ‘TRUE’

Value

A TraceQC object for the input will be returned.

Examples

## Not run: 
library(TraceQC)
obj <- generate_qc_report(
  input_file = system.file("extdata", "test_data",
                           "fastq", "example_14d.fastq.gz", package="TraceQC"),
  ref_file = system.file("extdata", "test_data",
                         "ref", "ref.txt", package="TraceQC"),
  preview = FALSE,
  title = "TraceQC report for example_14d.fastq.gz",
  ncores=1
  )
summary(obj)

## End(Not run)

LiuzLab/TraceQC documentation built on April 19, 2022, 1:29 p.m.