FastQCReporter: The FastQCReporter class

In HenrikBengtsson/aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

Description

Package: aroma.seq
Class FastQCReporter

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--AromaSeqTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--FileGroupsInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--FastQCReporter

Directly known subclasses:

public static class FastQCReporter
extends FileGroupsInterface

A FastQCReporter takes a FastqDataSet as input, possibly groups the samples, and generates FastQC [1] reports. How the grouping is done, can be controlled by a parameter.

Usage

FastQCReporter(dataSet=NULL, groupBy=NULL, ..., .className="FastqDataSet")

Arguments

dataSet	An FastqDataSet.
groupBy	A character string or an explicit named list, specifying which input files should be processed together.
...	Additional arguments passed to AromaSeqTransform.
.className	A character string specifying what class of data sets to accept.

Fields and Methods

Methods:

	getOutputDataSet	-
	process	-

Methods inherited from FileGroupsInterface:
getGroupBy, getGroupNames, getGroups, getInputDataSet, nbrOfGroups, validateGroups

Methods inherited from AromaSeqTransform:
as.character, findFilesTodo, getAcronym, getAsteriskTags, getFlavor, getFullName, getInputDataSet, getName, getOptionalArguments, getOrganism, getOutputDataSet, getParameters, getPath, getRootPath, getTags, isDone, length, process, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, findRspReportTemplate, asThis

Supported operating systems

This method is available on Linux, macOS, and Windows [1].

Author(s)

Henrik Bengtsson

References

[1] Simon Andrews, FastQC - A quality control tool for high throughput sequence data, March 2014. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

See Also

Internally mergeBam is used for merging, sorting, and indexing.

HenrikBengtsson/aroma.seq documentation built on Feb. 15, 2021, 2:21 a.m.