qrqc -- history of changes. Copyright (c) Vince Buffalo 2011-2012 Version 1.9.1: (2012-02-20) - plotQuals, plotBase, plotSeqLengths, plotGC replaced by qualPlot, basePlot, seqlenPlot, and gcPlot, respectively. These should be used for all plotting; these other functions are now deprecated. These new methods are all based on ggplot2. These new plotting functions now have methods for a named list of SequencySummary objects, which can be useful in comparing many sequence files at once. - There are also helper plotting functions scale_color_dna, scale_color_iupac, and geom_qlinerange for creating plots. - reportMethods now uses these new plotting methods. - New accessor functions getBase, getBaseProp, getQual, getSeqlen, and getMCQual can be used to return data frames of data from SequencySummary object. - Added function list2df for applying a function to objects in a named list and combining the results into a data frame. This is used in graphing lists of SequencySummary objects. - Removed Phred quality as a visible option in readSeqFile. I don't believe this should affect any users, but if it does, let me know.