LoadBackgroundErrorRate

char, name of the Rdata file containing the three variables <code>pos_ind</code>, <code>pos_snp</code>, <code>pos_ranges</code> as build by the function <code>PrepareLibrary</code>. Default NULL, use the position_ranges.rda provides that we used for our analysis.

pos_ranges.file, 

char, pathname of the file providing the background error rates obtained from the controls (default NULL use the provided background error rates obtained from our 29 controls). See <code>background_error_rate.txt</code> data and <code>BuildCtrlErrorRate</code> function.

ber.ctrl.file, 

integer, number of base positions trimmed at the ends of each amplicon (default 8)

n.trim, 

This function will load the background error rates created from the controls using the function BuildCtrlErrorRate

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.

LoadBackgroundErrorRate: function LoadBackgroundErrorRate

Description

Usage

Arguments

Value

References