getModule,FastqcData-method {ngsReports} | R Documentation

## Retrieve a given module from a Fastqc* Object

### Description

Retrieve a specific module from a Fastqc* object as a data.frame

### Usage

    ## S4 method for signature 'FastqcData'
    getModule(object, module)

    ## S4 method for signature 'FastqcDataList'
    getModule(object, module)

    ## S4 method for signature 'ANY'
    getModule(object, module)

### Arguments

`object` | Can be a `FastqcData`, `fastqcDataList`, or simply a `character` vector of paths
`module` | The requested module as contained in a FastQC report. Possible values are `Summary`, `Basic_Statistics`, `Per_base_sequence_quality`, `Per_tile_sequence_quality`, `Per_sequence_quality_scores`, `Per_base_sequence_content`, `Per_sequence_GC_content`, `Per_base_N_content`, `Sequence_Length_Distribution`, `Sequence_Duplication_Levels`, `Overrepresented_sequences`, `Adapter_Content`, `Kmer_Content`, `Total_Deduplicated_Percentage`. Note that spelling and capitalisation is exactly as contained within a FastQC report, with the exception that spaces have been converted to underscores. Partial matching is implemented for this argument.

### Details

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

### Value

A single `tibble` containing module-level information from all FastQC reports contained in the Fastqc* object.

### Examples

    # 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")

[Package ngsReports version 1.2.0 Index]