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)

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

## Not run: ------------------------------------ # # 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) ## ---------------------------------------------