FastqcData-class {ngsReports} | R Documentation

## The FastqcData Object Class

### Description

The FastqcData Object Class

### Usage

    FastqcData(x)

### Arguments

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

### Details

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.

### Value

An object of class FastqcData

### Slots

`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#'

### Examples

    # 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

[Package ngsReports version 1.0.1 Index]