BuildCtrlErrorRate      function BuildCtrlErrorRate
DetectPlasmaMutation    function DetectPlasmaMutation
LoadBackgroundErrorRate
                        function LoadBackgroundErrorRate
MAF_from_BAM            function MAF_from_BAM
PrepareLibrary          function PrepareLibrary
background_error_rate   The package provide the SNV and INDEL PERs
                        computed for the Ion AmpliSeq™ Colon and Lung
                        Cancer Panel v2 from 29 controls in a table
                        available in the data file
                        'background_error_rate.txt'.
hotspot                 The package provide a list of known hotspot
                        positions located on the amplicons of the Ion
                        AmpliSeq™ Colon and Lung Cancer Panel v2 as a
                        txt file 'hotspot.txt' which contains a
                        vector/variable -named chrpos (first row)- of
                        chars, of the form chrN:XXXXXXXXX defining
                        genomic positions.
positions_ranges        The package provide the positions and ranges
                        computed for the Ion AmpliSeq™ Colon and Lung
                        Cancer Panel v2 as a Rdata file
                        'positions_ranges.rda'.
