getSummary,.FastqcFile-method {ngsReports} | R Documentation |
Read the information from the summary.txt
files in each
.FastqcFile
## S4 method for signature '.FastqcFile' getSummary(object) ## S4 method for signature 'ANY' getSummary(object) ## S4 method for signature 'FastqcData' getSummary(object) ## S4 method for signature 'FastqcDataList' getSummary(object)
object |
Can be a |
This simply extracts the summary of PASS/WARN/FAIL status for every module as defined by the tool FastQC for each supplied file.
A tibble
containing the PASS/WARN/FAIL status for each
module, as defined in a FastQC report.
# Get the files included with the package packageDir <- system.file("extdata", package = "ngsReports") fl <- list.files(packageDir, pattern = "fastqc.zip", full.names = TRUE) # Load the FASTQC data as a FastqcDataList object fdl <- FastqcDataList(fl) # Return a tibble/tibble with the raw information getSummary(fdl)