A JunctionSeqCountSet is a container class that contains all information pertaining to a JunctionSeq analysis and dataset. In general, these methods and slots will not be used by the end-users. In general, JunctionSeqCountSet objects will be created by readJunctionSeqCounts or runJunctionSeqAnalyses and are to be manipulated byhigh-level JunctionSeq functions such as estimateEffectSizes or fitJunctionSeqDispersionFunction.
● Data Source:
BioConductor
● Keywords: classes
● Alias: JunctionSeqCountSet, JunctionSeqCountSet-class
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Saves a large battery of plots displaying the analysis results, for the purposes of data visualization. By default it saves a full set of plots for every gene that shows statistical significance and the adjusted-p < 0.01 level. Alternatively, it can be supplied with a specific gene list using the gene.list parameter, and will plot those specific genes.
● Data Source:
BioConductor
● Keywords:
● Alias: buildAllPlots
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Generates and saves one or more plots, displaying counts or averages for all counting bins across one particular gene. The parameters expr.plot, normCounts.plot, rExpr.plot, and rawCounts.plot determine which plot types are to be generated, and the parameters with.TX and without.TX determines whether these plots should include or not include the full transcript information, or if separate plots should be generated with and without the full transcript information.
● Data Source:
BioConductor
● Keywords:
● Alias: buildAllPlotsForGene
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This function runs fits another generalized linear model to the data, this one intended for use in estimating the effect sizes and expression estimates for each analysis.
● Data Source:
BioConductor
● Keywords:
● Alias: estimateEffectSizes
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This method estimates the sample dispersion for each counting bin (in other words, each splice junction locus).
● Data Source:
BioConductor
● Keywords:
● Alias: estimateJunctionSeqDispersions
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Estimate size factors, which are scaling factors used as "offsets" by the statistical model to make the different samples comparable. This is necessary because the different samples may have been sequenced to slightly different depths. Additionally, the presence of differentially expressed genes may cause the apparent depth of many genes to appear different.
● Data Source:
BioConductor
● Keywords:
● Alias: estimateJunctionSeqSizeFactors, writeSizeFactors
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Fit dispersion function to share dispersion information between features across the genome.
● Data Source:
BioConductor
● Keywords:
● Alias: fitJunctionSeqDispersionFunction
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Plots the countbin-specific estimated dispersion and the fitted dispersion curve.
● Data Source:
BioConductor
● Keywords:
● Alias: plotDispEsts
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Creates one results plot for one gene. Note that this function does not call a plotting device, so it will simply plot to the "current" device. If you want to automatically save images to file, use buildAllPlotsForGene, which internally calls this function.
● Data Source:
BioConductor
● Keywords:
● Alias: plotJunctionSeqResultsForGene
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Generates an MA-plot, which graphs the fold change versus the mean normalized expression. Statistically significant features are colored red.
● Data Source:
BioConductor
● Keywords:
● Alias: plotMA
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providing 
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