Class SequencingQcMetrics

java.lang.Object

ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics

public final class SequencingQcMetrics
extends Object

Per-sample sequencing QC metrics for one experiment, read out of the RNA-Seq pipeline's MultiQC report and joined to the experiment's BioAssays.

These are independent of expression similarity, which is the outlier detector's only input, so they are the second piece of evidence a curator has when judging a low-correlation sample. They are display-only: nothing here feeds OutlierDetectionService.

See Also:

• SequencingQcMetricsService

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static final class	SequencingQcMetrics.MetricDefinition	A metric column as MultiQC describes it.
static final class	SequencingQcMetrics.RunMetrics	One report row below the sample level — a sequencing run, or one mate of a paired run.
static final class	SequencingQcMetrics.SampleMetrics	The metrics resolved for a single bioAssay.

Constructor Summary

Constructors

Constructor	Description
SequencingQcMetrics(boolean reportPresent, List<SequencingQcMetrics.MetricDefinition> metrics, List<SequencingQcMetrics.SampleMetrics> samples, List<String> unmatchedKeys)	Creates a new SequencingQcMetrics instance.

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object o)
List<SequencingQcMetrics.MetricDefinition>	getMetrics()	Definitions for the metric names appearing in SequencingQcMetrics.SampleMetrics.getValues(), in the order MultiQC lists them.
List<SequencingQcMetrics.SampleMetrics>	getSamples()	One entry per BioAssay of the experiment, ordered by bioAssay id.
List<String>	getUnmatchedKeys()	Report row keys that could not be matched to any bioAssay of the experiment.
int	hashCode()
boolean	isReportPresent()	True when a MultiQC report was found and parsed.
String	toString()

Methods inherited from class Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Details

SequencingQcMetrics

public SequencingQcMetrics(boolean reportPresent,
 List<SequencingQcMetrics.MetricDefinition> metrics,
 List<SequencingQcMetrics.SampleMetrics> samples,
 List<String> unmatchedKeys)

Creates a new SequencingQcMetrics instance.

Parameters:

reportPresent - True when a MultiQC report was found and parsed. When false the rows carry only what the database itself holds (see SequencingQcMetrics.SampleMetrics.getReadCount()).

metrics - Definitions for the metric names appearing in SequencingQcMetrics.SampleMetrics.getValues(), in the order MultiQC lists them. A metric present in the data but absent from MultiQC's general-stats headers still gets an entry here, with only its name filled in.

samples - One entry per BioAssay of the experiment, ordered by bioAssay id. Assays the report says nothing about are still present, with an empty SequencingQcMetrics.SampleMetrics.getValues().

unmatchedKeys - Report row keys that could not be matched to any bioAssay of the experiment. Most are SRA run accessions (SRR…), which the FASTQ-level modules key by and which Gemma does not record; a caller cannot resolve them either, so they are reported rather than silently dropped. Sorted, and each key appears once however many modules used it.

Method Details

isReportPresent

public boolean isReportPresent()

True when a MultiQC report was found and parsed. When false the rows carry only what the database itself holds (see SequencingQcMetrics.SampleMetrics.getReadCount()).

getMetrics

public List<SequencingQcMetrics.MetricDefinition> getMetrics()

Definitions for the metric names appearing in SequencingQcMetrics.SampleMetrics.getValues(), in the order MultiQC lists them. A metric present in the data but absent from MultiQC's general-stats headers still gets an entry here, with only its name filled in.

getSamples

public List<SequencingQcMetrics.SampleMetrics> getSamples()

One entry per BioAssay of the experiment, ordered by bioAssay id. Assays the report says nothing about are still present, with an empty SequencingQcMetrics.SampleMetrics.getValues().

getUnmatchedKeys

public List<String> getUnmatchedKeys()

Report row keys that could not be matched to any bioAssay of the experiment. Most are SRA run accessions (SRR…), which the FASTQ-level modules key by and which Gemma does not record; a caller cannot resolve them either, so they are reported rather than silently dropped. Sorted, and each key appears once however many modules used it.

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object