Filter out clustered sequence variants

Sequence variants of multiple allele types (e.g., A -> G, A -> C) proximal to a putative editing site can be indicative of a region prone to mis-alignment artifacts. Sites will be removed if variants of multiple allele types are present within a given distance in genomic or transcriptome coordinate space.

Usage

filter_clustered_variants(
  rse,
  txdb,
  regions = c("transcript", "genome"),
  variant_dist = 100
)

Arguments

rse

SummarizedExperiment::SummarizedExperiment containing editing sites

txdb

GenomicFeatures::TxDb

regions

One of transcript or genome, specifying the coordinate system for calculating distances between variants.

variant_dist

distance in nucleotides for determining clustered variants

Value

SummarizedExperiment::SummarizedExperiment with sites removed from object dependent on filtering applied.

See also

Other se-filters: filter_multiallelic(), filter_splice_variants()

Examples

if(require("txdbmaker")){
  rse_adar_ifn <- mock_rse()
  rse <- rse_adar_ifn[seqnames(rse_adar_ifn) == "SPCS3"]
 
  # mock up a txdb with genes
  gr <- GRanges(c(
      "SPCS3:100-120:-",
      "SPCS3:325-350:-"
  ))
  gr$source <- "raer"
  gr$type <- "exon"
  gr$source <- NA
  gr$phase <- NA_integer_
  gr$gene_id <- c(1, 2)
  gr$transcript_id <- c("1.1", "2.1")
  txdb <- txdbmaker::makeTxDbFromGRanges(gr)
 
  rse <- filter_multiallelic(rse)
  filter_clustered_variants(rse, txdb, variant_dist = 10)

}
#> Loading required package: txdbmaker
#> Loading required package: GenomicFeatures
#> Loading required package: AnnotationDbi
#> 
#> Attaching package: ‘txdbmaker’
#> The following objects are masked from ‘package:GenomicFeatures’:
#> 
#>     UCSCFeatureDbTableSchema, browseUCSCtrack, getChromInfoFromBiomart,
#>     makeFDbPackageFromUCSC, makeFeatureDbFromUCSC, makePackageName,
#>     makeTxDb, makeTxDbFromBiomart, makeTxDbFromEnsembl,
#>     makeTxDbFromGFF, makeTxDbFromGRanges, makeTxDbFromUCSC,
#>     makeTxDbPackage, makeTxDbPackageFromBiomart,
#>     makeTxDbPackageFromUCSC, supportedMiRBaseBuildValues,
#>     supportedUCSCFeatureDbTables, supportedUCSCFeatureDbTracks,
#>     supportedUCSCtables
#> ℹ `filter_multiallelic()`: removed 0 sites from 8 (8 remain)
#> ℹ `filter_clustered_variants()`:  removed 3 sites from 8 (5 remain)
#> class: RangedSummarizedExperiment 
#> dim: 5 2 
#> metadata(0):
#> assays(7): ALT nRef ... nC nG
#> rownames(5): site_SPCS3_99_1 site_SPCS3_227_1 site_SPCS3_241_1
#>   site_SPCS3_329_1 site_SPCS3_330_1
#> rowData names(5): REF rpbz vdb sor ALT
#> colnames(2): wt adar1_ko
#> colData names(1): sample