package rnaseq
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class
CollectErccMetrics
extends FgBioTool with LazyLogging
 Annotations
 @ClpAnnotation()

case class
ErccDetailedMetric
(name: String, concentration: Double, count: Long, normalized_count: Double) extends Metric with Product with Serializable
Metrics produced by
CollectErccMetrics
describing various pertranscript metrics related to the spikein of ERCC (External RNA Controls Consortium) into an RNASeq experiment.Metrics produced by
CollectErccMetrics
describing various pertranscript metrics related to the spikein of ERCC (External RNA Controls Consortium) into an RNASeq experiment. One metric per ERCC transcript will be present. name
the name (or ID) of the ERCC transcript.
 concentration
the expected concentration as input to
CollectErccMetrics
. count
the observed count of the number of read pairs (or single end reads) .
 normalized_count
the observed count of the number of read pairs (or single end reads) normalized by the ERCC transcript length.
 sealed trait ErccMixture extends EnumEntry

case class
ErccSummaryMetrics
(total_reads: Long, ercc_reads: Long, fraction_ercc_reads: Double, ercc_templates: Long, total_transcripts: Int, passing_filter_transcripts: Int, pearsons_correlation: Option[Double], spearmans_correlation: Option[Double], intercept: Option[Double], slope: Option[Double], r_squared: Option[Double]) extends Metric with Product with Serializable
Metrics produced by
CollectErccMetrics
describing various summary metrics related to the spikein of ERCC (External RNA Controls Consortium) into an RNASeq experiment.Metrics produced by
CollectErccMetrics
describing various summary metrics related to the spikein of ERCC (External RNA Controls Consortium) into an RNASeq experiment.The correlation coefficients and linear regression are calculated based on the log2 observed read pair count normalized by ERCC transcript length versus the log2 expected concentration.
 total_reads
the total number of reads considered.
 ercc_reads
the total number of reads mapping to an ERCC transcript.
 fraction_ercc_reads
the fraction of total reads that map to an ERCC transcript.
 ercc_templates
the total number of read pairs (or single end reads) mapping to an ERCC transcript.
 total_transcripts
the total number of ERCC transcripts with at least one read observed.
 passing_filter_transcripts
the total number of ERCC transcripts with at least the userset minimum # of reads observed.
 pearsons_correlation
Pearson's correlation coefficient for correlation of concentration and normalized counts.
 spearmans_correlation
Spearman's correlation coefficient for correlation of concentration and normalized counts.
 intercept
the intercept of the linear regression.
 slope
the slope of the linear regression.
 r_squared
the rsquared of the linear regression.

class
EstimateRnaSeqInsertSize
extends FgBioTool with LazyLogging
 Annotations
 @ClpAnnotation()

case class
InsertSizeMetric
(pair_orientation: PairOrientation, read_pairs: Long = 0, mean: Double = 0, standard_deviation: Double = 0, median: Double = 0, min: Long = 0, max: Long = 0, median_absolute_deviation: Double = 0) extends Metric with Product with Serializable
Metrics produced by
EstimateRnaSeqInsertSize
to describe the distribution of insert sizes within an RNAseq experiment.Metrics produced by
EstimateRnaSeqInsertSize
to describe the distribution of insert sizes within an RNAseq experiment. The insert sizes are computed in "transcript space", accounting for spliced alignments, in order to get a true estimate of the size of the DNA fragment, not just it's span on the genome. pair_orientation
The orientation of the reads within a readpair relative to each other. Possible values are FR, RF and TANDEM.
 read_pairs
The number of read pairs observed with the
pair_orientation
. mean
The mean insert size of the read pairs.
 standard_deviation
The standard deviation of the insert size of the read pairs.
 median
The median insert size of the read pairs.
 min
The minimum observed insert size of the read pairs.
 max
The maximum observed insert size of the read pairs.
 median_absolute_deviation
The median absolution deviation of the read pairs.
Value Members
 object CollectErccMetrics
 object ErccMixture extends FgBioEnum[ErccMixture]
 object EstimateRnaSeqInsertSize