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Filter out sites near splice sites

Source: R/filter_rse.R
filter_splice_variants.Rd

Remove editing sites found in regions proximal to annotated splice junctions.

Usage

filter_splice_variants(rse, txdb, splice_site_dist = 4, ignore.strand = FALSE)

Arguments

rse

SummarizedExperiment::SummarizedExperiment with editing sites

txdb

GenomicFeatures::TxDb

splice_site_dist

distance to splice site

ignore.strand

if TRUE, ignore strand when comparing editing sites to splice sites

Value

SummarizedExperiment::SummarizedExperiment with sites adjacent to splice sites removed.

See also

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

Examples

if(require("txdbmaker")) {
  rse_adar_ifn <- mock_rse()
 
  # mock up a txdb with genes
  gr <- GRanges(c(
      "DHFR:310-330:-",
      "DHFR:410-415:-",
      "SSR3:100-155:-",
      "SSR3:180-190:-"
  ))
  gr$source <- "raer"
  gr$type <- "exon"
  gr$source <- NA
  gr$phase <- NA_integer_
  gr$gene_id <- c(1, 1, 2, 2)
  gr$transcript_id <- rep(c("1.1", "2.1"), each = 2)
  txdb <- txdbmaker::makeTxDbFromGRanges(gr)
 
  filter_splice_variants(rse_adar_ifn, txdb)
}
#> ℹ `filter_splice_variants()`:  removed 5 sites from 74 (69 remain)
#> class: RangedSummarizedExperiment 
#> dim: 69 2 
#> metadata(0):
#> assays(7): ALT nRef ... nC nG
#> rownames(69): site_SSR3_102_2 site_SSR3_125_2 ... site_DHFR_430_2
#>   site_DHFR_513_2
#> rowData names(4): REF rpbz vdb sor
#> colnames(2): wt adar1_ko
#> colData names(1): sample