Tumor Mutation Detection in Plasma using Barcoding

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Documentation for package ‘PlasmaMutationDetector2’ version 1.1.11

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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'.
background_error_rate.txt 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'.
BuildCtrlErrorRate function BuildCtrlErrorRate
DetectPlasmaMutation function DetectPlasmaMutation
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.
hotspot.txt 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.
LoadBackgroundErrorRate function LoadBackgroundErrorRate
MAF_from_BAM function MAF_from_BAM
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'.
positions_ranges.rda 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'.
pos_ind 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'.
pos_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'.
pos_snp 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'.
PrepareLibrary function PrepareLibrary