LoadBackgroundErrorRate {PlasmaMutationDetector}

function LoadBackgroundErrorRate

Description

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

Usage

LoadBackgroundErrorRate(pos_ranges.file, ber.ctrl.file, n.trim)

Arguments

pos_ranges.file

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

ber.ctrl.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 background_error_rate.txt data and BuildCtrlErrorRate function.

n.trim

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

Value

the adapted background error rate

Author(s)

N. Pécuchet, P. Laurent-Puig and Y. Rozenholc

References

Analysis of base-position error rate of next-generation sequencing to detect tumor mutations in circulating DNA N. Pécuchet, Y. Rozenholc, E. Zonta, D. Pietraz, A. Didelot, P. Combe, L. Gibault, J-B. Bachet, V. Taly, E. Fabre, H. Blons, P. Laurent-Puig in Clinical Chemistry