Description Usage Arguments Value Author(s) References Examples
Read BAM files and create MAF file. BAMfiles are stored in a sub-folder '/rBAM'. MAF files are intermediate files stored in a sub-folder '/BER'. MAF files contain the raw counts of A,T,C,G, insertion, deletion, insertion>2bp, deletion >2bp for strand plus and stand minus. Note : we strongly recommand to externally recalibrate BAM files using tools like GATK.
1 2 3 | MAF_from_BAM(study.dir = "Plasma/", input.filenames = NULL,
bai.ext = ".bai", pos_ranges.file = NULL, force = FALSE,
output.dir = study.dir)
|
study.dir, |
char, name of the folder containing the rBAM directory (default 'Plasma/'). The typical folder hierarchy will consist of 'Plasma/rBAM' |
input.filenames, |
a vector of char (default NULL), the names of the BAM files to process. If NULL all BAM files in the rBAM folder will be processed |
bai.ext, |
char, filename extension of the bai files (default '.bai') |
pos_ranges.file, |
char, name of the Rdata file containing the three variables |
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 path/names of the MAF 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
MAF_from_BAM(ctrl.dir,force=TRUE,output.dir=paste0(tempdir(),'/'))
## End(Not run)
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