class:FastQC

FastQC-class

class:SequenceQC

SequenceQC-class

class:SequenceQCSet

SequenceQCSet-class

readFastQC

SequenceQCSet

Basic_Statistics

Per_base_sequence_quality

Per_sequence_quality_scores

Per_base_sequence_content

Per_base_GC_content

Per_sequence_GC_content

Per_base_N_content

Sequence_Length_Distribution

Sequence_Duplication_Levels

Overrepresented_sequences

Mismatches

MismatchTable

show,FastQC-method

Basic_Statistics,FastQC-method

Per_base_sequence_quality,FastQC-method

Per_sequence_quality_scores,FastQC-method

Per_base_sequence_content,FastQC-method

Per_base_GC_content,FastQC-method

Per_sequence_GC_content,FastQC-method

Per_base_N_content,FastQC-method

Sequence_Length_Distribution,FastQC-method

Sequence_Duplication_Levels,FastQC-method

Overrepresented_sequences,FastQC-method

show,SequenceQC-method

Basic_Statistics,SequenceQC-method

Per_base_sequence_quality,SequenceQC-method

Per_sequence_quality_scores,SequenceQC-method

Per_base_sequence_content,SequenceQC-method

Per_base_GC_content,SequenceQC-method

Per_sequence_GC_content,SequenceQC-method

Per_base_N_content,SequenceQC-method

Sequence_Length_Distribution,SequenceQC-method

Sequence_Duplication_Levels,SequenceQC-method

Overrepresented_sequences,SequenceQC-method

Mismatches,SequenceQC-method

MismatchTable,SequenceQC-method

show,SequenceQCSet-method

Basic_Statistics,SequenceQCSet-method

Per_base_sequence_quality,SequenceQCSet-method

Per_sequence_quality_scores,SequenceQCSet-method

Per_base_sequence_content,SequenceQCSet-method

Per_base_GC_content,SequenceQCSet-method

Per_sequence_GC_content,SequenceQCSet-method

Per_base_N_content,SequenceQCSet-method

Sequence_Length_Distribution,SequenceQCSet-method

Sequence_Duplication_Levels,SequenceQCSet-method

Overrepresented_sequences,SequenceQCSet-method

Mismatches,SequenceQCSet-method

MismatchTable,SequenceQCSet-method

[,SequenceQCSet,ANY,missing,ANY-method


	The FastQC class stores results obtained from the FastQC application (see <code>references</code>),
	with a slot for each FastQC module. The SequenceQC class contains the QC results of a single lane of sequencing in three slots:
	<code>Unaligned</code> - FastQC results obtained from all reads (before alignment) 
	<code>Aligned</code> - FastQC results obtained from only reads which aligned
	<code>Mismatches</code> - a <code>data.frame</code> containing counts for the number of mismatches of each type found at each sequencing cycle   


Tools for the analysis of enrichment-based epigenomic
data.  Features include summarization and visualization of
epigenomic data across promoters according to gene expression
context, finding regions of differential methylation/binding,
BayMeth for quantifying methylation etc.

Mark Robinson

Repitools

Epigenomic tools

FastQC-class function

<code>Basic_Statistics</code> <code>Per_base_sequence_quality</code> <code>Per_sequence_quality_scores</code> <code>Per_base_sequence_content</code> <code>Per_base_GC_content</code> <code>Per_sequence_GC_content</code> <code>Per_base_N_content</code> <code>Sequence_Length_Distribution</code> <code>Sequence_Duplication_Levels</code> <code>Overrepresented_sequences</code>

Slots of a FastQC object

<code>Unaligned</code> - FastQC results obtained from all reads (before alignment) <code>Aligned</code> - FastQC results obtained from only reads which aligned <code>Mismatches</code> - a <code>data.frame</code> containing counts for the number of mismatches of each type found at each sequencing cycle <code>MismatchTable</code> - a <code>data.frame</code> containing counts of how many mismatches aligned sequences contain

Slots of a SequenceQC object

The FastQC class stores results obtained from the FastQC application (see <code>references</code>),
	with a slot for each FastQC module. The SequenceQC class contains the QC results of a single lane of sequencing in three slots:
	<code>Unaligned</code> - FastQC results obtained from all reads (before alignment) 
	<code>Aligned</code> - FastQC results obtained from only reads which aligned
	<code>Mismatches</code> - a <code>data.frame</code> containing counts for the number of mismatches of each type found at each sequencing cycle

FastQC and associated classes

FastQC-class: FastQC and associated classes

Description

Arguments

Slots of a FastQC object

Slots of a SequenceQC object

References