| Type: | Package |
| Title: | Reversion Mutation Detector for DNA Sequencing Data |
| Version: | 1.0.0 |
| Date: | 2025-12-16 |
| Author: | Hui Xiao [aut, cre], Stephen Pettitt [aut], Syed Haider [aut] |
| Maintainer: | Hui Xiao <hui.xiao@icr.ac.uk> |
| Description: | Reversion mutations are secondary mutations that reverse the deleterious effects of an original pathogenic mutation, partially or fully restoring the gene's function. The revert package detects reversion mutations for a specific pathogenic mutation from DNA-seq bam files. |
| Depends: | R (≥ 4.4.0) |
| License: | GPL-2 |
| Imports: | BSgenome, BiocGenerics, Biostrings, GenomeInfoDb, GenomicRanges, IRanges, Rsamtools, S4Vectors, ensembldb, pwalign, stats, utils |
| Suggests: | knitr, rmarkdown, futile.logger, BSgenome.Hsapiens.UCSC.hg19, EnsDb.Hsapiens.v75, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86 |
| RoxygenNote: | 7.3.2 |
| Encoding: | UTF-8 |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2025-12-16 16:31:45 UTC; hxiao |
| Repository: | CRAN |
| Date/Publication: | 2025-12-17 23:30:02 UTC |
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