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Check reference compatibility between track data and genome specification

Source: R/referenceCheck.R
checkReferenceCompatibility.Rd

Compares contig naming conventions (e.g. UCSC chr1 vs Ensembl 1), contig lengths (e.g. hg19 vs hg38), and coordinate boundaries between a track (BAM, CRAM, VCF, BED, or Bioconductor object) and the active reference genome.

Usage

checkReferenceCompatibility(
  target,
  genomeName = NULL,
  genomeSpec = NULL,
  session = NULL,
  id = NULL
)

Arguments

target

A file path (.bam, .cram, .vcf, .vcf.gz, .bed) or data object (data.frame, GenomicAlignments, VCF, GRanges)

genomeName

Character string, e.g. "hg38", "hg19", "mm10"

genomeSpec

Named list of genome options, as produced by parseAndValidateGenomeSpec

session

Optional Shiny session object

id

Optional widget element ID

Value

A list with:

  • checked: logical indicating whether both inputs could be inspected

  • compatible: logical indicating if no critical mismatches were found, or NA when the inputs could not be checked

  • mismatches: character vector of descriptive warning messages

  • details: list of specific detected anomalies (naming, length, out-of-bounds)

  • targetAssembly: detected assembly of track, if recognized

  • referenceAssembly: reference genome name

Examples

bamFile <- system.file(package = "igvShiny", "extdata", "tumor.bam")
# tumor.bam is GRCh38: compatible with hg38, incompatible with hg19
res1 <- checkReferenceCompatibility(bamFile, genomeName = "hg38")
res1$compatible  # TRUE
#> [1] TRUE

res2 <- checkReferenceCompatibility(bamFile, genomeName = "hg19")
res2$compatible  # FALSE
#> [1] FALSE