getModule: Retrieve a given module from a Fastqc* Object

Description Usage Arguments Details Value Examples

Description

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

Usage

1
2
3
4
5
6
7
8
## 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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
# 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")

UofABioinformaticsHub/fastqcReports documentation built on Nov. 21, 2020, 7:44 p.m.