Tumor Mutation Detection in Plasma
The package provide the SNV and INDEL PERs computed for the Ion AmpliS...
function BuildCtrlErrorRate
function DetectPlasmaMutation
The package provide a list of known hotspot positions located on the a...
function LoadBackgroundErrorRate
function MAF_from_BAM
function PrepareLibrary
Aims at detecting single nucleotide variation (SNV) and insertion/deletion (INDEL) in circulating tumor DNA (ctDNA), used as a surrogate marker for tumor, at each base position of an Next Generation Sequencing (NGS) analysis. Mutations are assessed by comparing the minor-allele frequency at each position to the measured PER in control samples.