background_error_rate {PlasmaMutationDetector2}

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.

Description

This table contains 9 variables for each genomic position

• chrpos, char, of the form chrN:XXXXXXXXX defining genomic position

• N0, integer, the coverture in the controls

• E0, integer, the number of errors in the controls

• p.sain, numeric, the ratio E0/N0

• up.sain, numeric, the 95th quantile of the Binomial with parameter N0 and E0/N0

• E0indel, integer, the amount of indel

• indel.p.sain, numeric, the ration E0indel/N0

• indel.up.sain, numeric, the 95th quantile of the Binomial with parameter N0 and E0indel/N0

• hotspot, char, either 'Non-hotspot' or 'Hotspot' depending if the genomic position is known as hotspot or not.

Usage

data(background_error_rate)

Author(s)

N. Pécuchet, P. Laurent-Puig, O. Nordgård 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

Novel hybridization- and tag-based error-corrected method for sensitive ctDNA mutation detection using ion semiconductor sequencing Kjersti Tjensvoll, Morten Lapin, Bjørnar Gilje, Herish Garresori, Satu Oltedal, Rakel Brendsdal Forthun, Anders Molven, Yves Rozenholc and Oddmund Nordgård in Scientific Reports

See Also

BuildCtrlErrorRate