rpoplin 2b51cf18f0 AnalyzeAnnotations now outputs plots with log x-axis in addition to standard x-axis so things like DP and MQ0 are easier to see. AnalyzeAnnotations now skips over all annotations that aren't floating point values. Recalibrator now warns users if PL tags are missing and so therefore it is reverting to illumina. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2681 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-25 19:39:18 +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_BinnedTiTv.R	AnalyzeAnnotations now outputs plots with log x-axis in addition to standard x-axis so things like DP and MQ0 are easier to see. AnalyzeAnnotations now skips over all annotations that aren't floating point values. Recalibrator now warns users if PL tags are missing and so therefore it is reverting to illumina.	2010-01-25 19:39:18 +00:00
plot_Annotations_CumulativeTiTv.R	AnalyzeAnnotations now bins variants per each annotation and outputs plots of TiTv ratio as a function of the annotation's value.	2010-01-21 21:15:11 +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