background_error_rate {PlasmaMutationDetector}

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 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

See Also

BuildCtrlErrorRate