FastqcData: The FastqcData Object Class
In ngsReports: Load FastqQC reports and other NGS related files

Description Usage Arguments Details Value Slots Examples

The FastqcData Object Class \lifecyclestable

1	FastqcData(x)

`x`	Path to a single zip archive or extracted folder for a individual FastQC report.

This object class is the main object required for generating plots and tables. Instantiation will first test for a compressed file (or extracted directory) with the correct data structure, and will then parse all the data into R as a FastqcData object. FastQC modules are contained as individual slots, which can be viewed using slotNames.

Individual modules can be returned using the function getModule() and specifying which module is required. See getModule for more details.

An object of class FastqcData

Summary: Summary of PASS/WARN/FAIL status for each module
Basic_Statistics: The Basic_Statstics table from the top of a FastQC html report
Per_base_sequence_quality: The underlying data from the Per_base_sequence_quality module
Per_sequence_quality_scores: The underlying data from the Per_sequence_quality_scores module
Per_base_sequence_content: The underlying data from the Per_base_sequence_content module
Per_sequence_GC_content: The underlying data from the Per_sequence_GC_content module
Per_base_N_content: The underlying data from the Per_base_N_content module
Sequence_Length_Distribution: The underlying data from the Sequence_Length_Distribution module
Sequence_Duplication_Levels: The underlying data from the Sequence_Duplication_Levels module
Overrepresented_sequences: The underlying data from the Overrepresented_sequences module
Adapter_Content: The underlying data from the Adapter_Content module
Kmer_Content: The underlying data from the Kmer_Content module
Total_Deduplicated_Percentage: Estimate taken from the plot data for Sequence_Duplication_Levels. Only included in later versions of FastQC
version: The version of FastQC used for generation of the report (if available)
path: Path to the 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)[1]

# Load the FASTQC data as a FastqcData object
fd <- FastqcData(fl)
fd