getModule,FastqcData-method {ngsReports} | R Documentation |
Retrieve a specific module from a Fastqc* object as a data.frame
## S4 method for signature 'FastqcData' getModule(object, module) ## S4 method for signature 'FastqcDataList' getModule(object, module) ## S4 method for signature 'ANY' getModule(object, module)
object |
Can be a |
module |
The requested module as contained in a FastQC report. Possible
values are |
This function will return a given module from a Fastqc* object as a data.frame. Note that each module will be it's own unique structure, although all will return a data.frame
A single tibble
containing module-level information
from all FastQC reports contained in the Fastqc* object.
# 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) # Extract the Summary module, which corresponds to the PASS/WARN/FAIL flags getModule(fdl, "Summary") # The Basic_Statistics module corresponds to the table at the top of each # FastQC report getModule(fdl, "Basic_Statistics")