rpoplin 16da5011c0 Added a new option for indicating the mean number of variants on the AnalyzeAnnotations plots. This way one can say, for example, filtering at this point will keep 75 percent of all the variants. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2744 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-29 21:58:31 +00:00
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generateBySamplePlot.R	R script for graphing depth of coverage by sample name, and generating a loess curve for each sample's data.	2009-12-10 21:58:01 +00:00
plot_Annotations_BinnedTruthMetrics.R	Added a new option for indicating the mean number of variants on the AnalyzeAnnotations plots. This way one can say, for example, filtering at this point will keep 75 percent of all the variants.	2010-01-29 21:58:31 +00:00
plot_residualError_OtherCovariate.R	Update to AnalyzeCovariates to make the histogram of PairedReadOrder look a little nicer	2010-01-13 20:26:31 +00:00
plot_residualError_QualityScoreCovariate.R	Fixed an issue with recalibrating original quality scores above Q40. There is a new option -maxQ which sets the maximum quality score possible for when a RecalDatum tries to compute its quality score from the mismatch rate. The same option was added to AnalyzeCovariates to help with plotting q scores above Q40. Added an integration test which makes use of this new -maxQ option.	2010-01-07 13:50:30 +00:00
whole_exome_bait_selection.R	R script for selecting a variety of baits (using %GC content and normalized coverage) for Nanostring assessment from those used in the Agilent whole exome hybrid selection design.	2009-09-22 18:10:14 +00:00