# Tumor Mutation Detection in Plasma using Barcoding

## Documentation for package ‘PlasmaMutationDetector2’ version 1.1.11

- DESCRIPTION file.

## Help Pages

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