Description Usage Arguments Value Author(s) References Examples
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.
1 2 3 | BuildCtrlErrorRate(ctrl.dir = "Plasma ctrl/", bai.ext = ".bai",
pos_ranges.file = NULL, hotspot.file = NULL, force = FALSE,
output.dir = ctrl.dir)
|
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 |
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 |
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 |
the number of processed files
N. P<c3><a9>cuchet, P. Laurent-Puig and Y. Rozenholc
Analysis of base-position error rate of next-generation sequencing to detect tumor mutations in circulating DNA N. P<c3><a9>cuchet, 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
1 2 3 4 5 6 7 | ## 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)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.