getReversions() detects reversion mutations for a given pathogenic mutation from a BAM file of DNA sequencing data.
getReversions(
bam.file,
out.dir,
reference,
pathog.mut,
gene.name = NULL,
transcript.id = NULL,
detection.window = 100,
splice.region = 8,
check.soft.clipping = TRUE,
softClippedReads.realign.window = 1000,
softClippedReads.realign.match = 1,
softClippedReads.realign.mismatch = 4,
softClippedReads.realign.gapOpening = 6,
softClippedReads.realign.gapExtension = 0,
check.wildtype.reads = FALSE,
is.paired.end = TRUE,
keep.duplicate.reads = TRUE,
keep.secondary.alignment = TRUE,
keep.supplementary.alignment = TRUE,
minimum.mapping.quality = 0,
verbose = TRUE,
out.failed.reads = FALSE
)Results written into output directory:
".reversions.txt" contains all reversions identified for the pathogenic mutation from the BAM file.
".split_mutations.txt" contains information of each single mutation in a reversion.
".revert_assembly.bam" contains all reads realigned to the pathogenic mutation.
".revert_assembly.bam.bai" is the index file for '.revert_assembly.bam'.
".revert_settings.txt" contains the summary of running parameters and processed reads.
".failed_reads.txt" (optional) contains the names of reads failed for reversion detection.
For more details of the output files see the help vignette
A character file name of the BAM file containing aligned reads to be processed.
A character file path to write output files.
A character variable specifying the reference genome version (hg19, hg38, mm10) or a FASTA file containing the open reading frames of reference sequences.
A character variable specifying the genomic position of pathogenic mutation following the HGVS-like syntax for substitution, deletion, insertion, deletion-insertion (delins), or duplication.
A character gene name for the pathogenic mutation.
A character Ensembl Transcript ID for the pathogenic mutation.
A non-negative integer specifying the length of flanking regions to be added to both ends of pathogenic mutation locus for detecting reversion mutations. Default is 100.
A positive integer specifying the length of splicing junction region to be considered in introns. Default is 8.
A logical value indicating whether soft-clipped reads to be realigned. Default is TRUE.
A non-negative integer specifying the length of flanking regions to be added to both ends of pathogenic mutation locus for realigning soft-clipped reads. Default is 1000.
A non-negative integer specifying the scoring for a nucleotide match for realigning soft-clipped reads. Default is 1.
A non-negative integer specifying the scoring for a nucleotide mismatch for realigning soft-clipped reads. Default is 4.
A non-negative integer specifying the cost for opening a gap in the realignment of soft-clipped reads. Default is 6.
A non-negative integer specifying the incremental cost incurred along the length of the gap in the realignment of soft-clipped reads. Default is 0.
A logical value indicating whether wild type reads to be processed as revertant-to-wildtype reads. Default is FALSE.
A logical value indicating whether reads in BAM file are paired-end (TRUE) or single-end (FALSE). Default is TRUE.
A logical value indicating whether duplicated reads in the BAM file to be processed (TRUE) or discarded (FALSE). Default is TRUE.
A logical value indicating whether secondary alignment reads in the BAM file to be processed (TRUE) or discarded (FALSE). Default is TRUE.
A logical value indicating whether supplementary alignment reads in the BAM file to be processed (TRUE) or discarded (FALSE). Default is TRUE.
A non-negative integer specifying the minimum mapping quality of reads in the BAM file to be processed. Default is 0.
A logical value indicating whether progress logging to be printed to stdout. Default is TRUE.
A logical value indicating whether the name of failed reads to be written to the '.failed_reads.txt' file. Default is FALSE.
# \donttest{
getReversions(
bam.file = system.file("extdata", "toy_data_1.bam", package="revert"),
out.dir = tempdir(),
reference = "hg19",
pathog.mut = "chr13:g.32913319_32913320delTG",
gene.name = "BRCA2",
transcript.id = "ENST00000544455")
# }
# For more examples see the help vignette
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