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Apply strand correction using gene annotations

Source: R/calc_AEI.R
correct_strand.Rd

Gene annotations are used to infer the likely strand of editing sites. This function will operate on unstranded datasets which have been processed using "unstranded" library type which reports variants with respect to the + strand for all sites. The strand of the editing site will be assigned the strand of overlapping features in the genes_gr object. Sites with no-overlap, or overlapping features with conflicting strands (+ and -) will be removed.

Usage

correct_strand(rse, genes_gr)

Arguments

rse

RangedSummarizedExperiment object containing editing sites processed with "unstranded" setting

genes_gr

GRanges object containing reference features to annotate the strand of the editing sites.

Value

RangedSummarizedExperiment object containing pileup assays, with strand corrected based on supplied genomic intervals.

Examples

suppressPackageStartupMessages(library("GenomicRanges"))

bamfn <- raer_example("SRR5564269_Aligned.sortedByCoord.out.md.bam")
fafn <- raer_example("human.fasta")
fp <- FilterParam(library_type = "unstranded")
rse <- pileup_sites(bamfn, fafn, param = fp)

genes <- GRanges(c(
    "DHFR:200-400:+",
    "SPCS3:100-200:-",
    "SSR3:3-10:-",
    "SSR3:6-12:+"
))

correct_strand(rse, genes)
#> class: RangedSummarizedExperiment 
#> dim: 307 1 
#> metadata(0):
#> assays(7): ALT nRef ... nC nG
#> rownames(307): site_SSR3_3_1 site_SSR3_4_1 ... site_DHFR_399_1
#>   site_DHFR_400_1
#> rowData names(4): REF rpbz vdb sor
#> colnames(1): SRR5564269_Aligned.sortedByCoord.out.md.bam
#> colData names(1): sample