BuildCtrlErrorRate {PlasmaMutationDetector2}

function BuildCtrlErrorRate

Description

Compute the SNV Position-Error Rates and INDEL Position-Error Rates from control samples (available in the control directory ctrl.dir). This function requires MAF files, that will be automatically generated if not present in the specified control folder. SNV PER is computed as the sum in control samples of SNV background counts / sum in control samples of depths where SNV background counts = depth - major allele count. INDEL PER is computed as sum in control samples of INDEL background counts / sum in control samples of depths where INDEL background counts = sum of insertion and deletion counts.

Usage

BuildCtrlErrorRate(
  ctrl.dir = "Plasma ctrl/",
  bai.ext = ".bai",
  pos_ranges.file = NULL,
  hotspot.file = NULL,
  cov.min = 5000,
  force = FALSE,
  output.dir = ctrl.dir,
  n.trim = 0
)

Arguments

ctrl.dir

char, foldername containing the control files (default 'Plasma ctrl/'). The typical folder hierarchy will consist of 'Plasma ctrl/rBAM'

bai.ext

char, filename extension of the bai files (default '.bai')

pos_ranges.file

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

hotspot.file

char, name of the text file containing a list of the genomic positions of the hotspots (default NULL, read the provide hotspot.txt, see hotspot)

cov.min

integer, minimal coverture to take into account a position (default 5000)

force

boolean, (default FALSE) if TRUE force all computations to all files including already processed ones

output.dir

char, name of the folder to save results (default ctrl.dir).

n.trim

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

Value

the number of processed files

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 and 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

Examples

## Not run: 
   ctrl.dir = system.file("extdata", "4test_only/ctrl/", package = "PlasmaMutationDetector2")
   if (substr(ctrl.dir,nchar(ctrl.dir),nchar(ctrl.dir))!='/')
     ctrl.dir = paste0(ctrl.dir,'/') # TO RUN UNDER WINDOWS
   BuildCtrlErrorRate(ctrl.dir,output.dir=paste0(tempdir(),'/'))
   
## End(Not run)