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.
qc_report(
qc.path,
result.file,
experiment = NULL,
interpret = FALSE,
template = NULL,
preview = TRUE
)
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.
path to the result file prefix (e.g., path/to/qc-result). Don't add the file extension.
text specifying a short description of the experiment. For example experiment = "RNA sequencing of colon cancer cell lines".
logical value. If TRUE, adds the interpretation of each module.
a character vector specifying the path to an Rmd template. file.
logical value. If TRUE, shows a preview of the report.
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)
}