fastqcr (version 0.1.3)

qc_report: Build a QC Report

Description

Create an HTML file containing FastQC reports of one or multiple files. Inputs can be either a directory containing multiple FastQC reports or a single sample FastQC report.

Usage

qc_report(
  qc.path,
  result.file,
  experiment = NULL,
  interpret = FALSE,
  template = NULL,
  preview = TRUE
)

Arguments

qc.path

path to the FastQC reports. Allowed values include:

• A path to a directory containing multiple zipped FastQC reports,

• Or a single sample zipped FastQC report. Partial match is allowed for sample name.

result.file

path to the result file prefix (e.g., path/to/qc-result). Don't add the file extension.

experiment

text specifying a short description of the experiment. For example experiment = "RNA sequencing of colon cancer cell lines".

interpret

logical value. If TRUE, adds the interpretation of each module.

template

a character vector specifying the path to an Rmd template. file.

preview

logical value. If TRUE, shows a preview of the report.

Examples

if (FALSE) {
# Demo QC Directory
qc.path <- system.file("fastqc_results", package = "fastqcr")
qc.path

# List of files in the directory
list.files(qc.path)

# Multi QC report
qc_report(qc.path, result.file = "~/Desktop/result")

# QC Report of one sample with plot interpretation
 qc.file <- system.file("fastqc_results", "S1_fastqc.zip", package = "fastqcr")
 qc_report(qc.file, result.file = "~/Desktop/result",
   interpret = TRUE)
}