BuildCtrlErrorRate {PlasmaMutationDetector}

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, force = FALSE,
  output.dir = ctrl.dir)

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)

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).

Value

the number of processed files

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

Examples

## Not run: 
   ctrl.dir = system.file("extdata", "4test_only/ctrl/", package = "PlasmaMutationDetector")
   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)