Package 'revert'

Detect reversion mutations

Description

getReversions() detects reversion mutations for a given pathogenic mutation from a BAM file of DNA sequencing data.

Usage

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
)

Arguments

bam.file	A character file name of the BAM file containing aligned reads to be processed.
out.dir	A character file path to write output files.
reference	A character variable specifying the reference genome version (hg19, hg38, mm10) or a FASTA file containing the open reading frames of reference sequences.
pathog.mut	A character variable specifying the genomic position of pathogenic mutation following the HGVS-like syntax for substitution, deletion, insertion, deletion-insertion (delins), or duplication.
gene.name	A character gene name for the pathogenic mutation.
transcript.id	A character Ensembl Transcript ID for the pathogenic mutation.
detection.window	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.
splice.region	A positive integer specifying the length of splicing junction region to be considered in introns. Default is 8.
check.soft.clipping	A logical value indicating whether soft-clipped reads to be realigned. Default is TRUE.
softClippedReads.realign.window	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.
softClippedReads.realign.match	A non-negative integer specifying the scoring for a nucleotide match for realigning soft-clipped reads. Default is 1.
softClippedReads.realign.mismatch	A non-negative integer specifying the scoring for a nucleotide mismatch for realigning soft-clipped reads. Default is 4.
softClippedReads.realign.gapOpening	A non-negative integer specifying the cost for opening a gap in the realignment of soft-clipped reads. Default is 6.
softClippedReads.realign.gapExtension	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.
check.wildtype.reads	A logical value indicating whether wild type reads to be processed as revertant-to-wildtype reads. Default is FALSE.
is.paired.end	A logical value indicating whether reads in BAM file are paired-end (TRUE) or single-end (FALSE). Default is TRUE.
keep.duplicate.reads	A logical value indicating whether duplicated reads in the BAM file to be processed (TRUE) or discarded (FALSE). Default is TRUE.
keep.secondary.alignment	A logical value indicating whether secondary alignment reads in the BAM file to be processed (TRUE) or discarded (FALSE). Default is TRUE.
keep.supplementary.alignment	A logical value indicating whether supplementary alignment reads in the BAM file to be processed (TRUE) or discarded (FALSE). Default is TRUE.
minimum.mapping.quality	A non-negative integer specifying the minimum mapping quality of reads in the BAM file to be processed. Default is 0.
verbose	A logical value indicating whether progress logging to be printed to stdout. Default is TRUE.
out.failed.reads	A logical value indicating whether the name of failed reads to be written to the '.failed_reads.txt' file. Default is FALSE.

Value

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

Examples

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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