DetectPlasmaMutation {PlasmaMutationDetector2}

function DetectPlasmaMutation

Description

This is the main function of the package that calls mutations by comparing at each genomic position the SNV or INDEL frequencies computed in one tested sample to the SNV or INDEL Position-Error Rates computed from several control samples by a binomial test. An outlier detection is performed among all intra-sample p-values to call a mutation. For users wishing to develop their own analysis for other sequencing panel, it requires recalibrated BAM files control samples to be processed to compute the Position-Error Rates stored in a file specified in ber.ctrl.file.

Usage

DetectPlasmaMutation(
  patient.dir = "./",
  patient.name = NULL,
  pos_ranges.file = NULL,
  ber.ctrl.file = NULL,
  bai.ext = ".bai",
  alpha = 0.05,
  n.trim = 0,
  force = FALSE,
  show.more = FALSE,
  qcutoff.snv = 1,
  qcutoff.indel = 1,
  cutoff.sb.hotspot = Inf,
  cutoff.sb.nonhotspot = cutoff.sb.hotspot,
  cutoff.sb.indel = cutoff.sb.hotspot,
  cutoff.sb.ref = 0.9,
  hotspot.indel = "chr7:55227950:55249171",
  output.dir = patient.dir
)

Arguments

patient.dir

char, foldername containing the rBAM folder of the patients. The typical folder hierarchy will consist of 'Plasma/rBAM'

patient.name

char, filename of the patient .bam file(s) (default NULL read all patients in folder patient.dir)

pos_ranges.file

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

ber.ctrl.file

char, pathname of the file providing the background error rates obtained from the controls (default NULL use the provided background error rates obtained from our 29 controls). See background_error_rate.txt data and BuildCtrlErrorRate function.

bai.ext

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

alpha

num, global false positive rate = global test level (default 0.05)

n.trim

integer, number of base positions trimmed at the ends of each amplicon (default 0)

force

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

show.more

boolean, (default FALSE show only detected positions) if TRUE additional annotations on result plots are given for non-significant mutations

qcutoff.snv

numeric, proportion of kept base positions ranged by increasing percentile SNV PER in control samples (default 1)

qcutoff.indel

numeric, proportion of kept base positions ranged by increasing percentile INDEL PER in control samples (default 1)

cutoff.sb.hotspot

numeric, exclude hotspot positions without Symmetric Odds Ratio test < cutoff (default 1)

cutoff.sb.nonhotspot

numeric, exclude non-hotspot positions without Symmetric Odds Ratio test < cutoff (default cutoff.sb.hotspot)

cutoff.sb.indel

numeric, exclude indel positions without Symmetric Odds Ratio test < cutoff (default cutoff.sb.hotspot)

cutoff.sb.ref

numeric, exclude ref positions without Symmetric Odds Ratio test < cutoff (default cutoff = 0.9)

hotspot.indel

char, a vector containing the known positions of hotspot deletion/insertion defined as chrX:start:end (default 'chr7:55227950:55249171')

output.dir

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

Value

the number of processed patients

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

     patient.dir=system.file("extdata","4test_only/case/",package="PlasmaMutationDetector2")
     if (substr(patient.dir,nchar(patient.dir),nchar(patient.dir))!='/')
       patient.dir = paste0(patient.dir,'/') # TO RUN UNDER WINDOWS
     DetectPlasmaMutation(patient.dir,output.dir=paste0(tempdir(),'/'))