Annotate a VCF data frame with transcript strand information

For each variant, finds overlapping transcripts in trans_ranges via GenomicRanges::findOverlaps() with type = "within", and appends columns trans.start.pos, trans.end.pos, trans.strand, trans.Ensembl.gene.ID, trans.gene.symbol, plus bothstrand (TRUE if the variant falls on transcripts from both strands) and count (number of overlapping transcripts).

Usage

add_transcript_strand(df, ref_genome, trans_ranges = NULL, name_of_vcf = NULL)

Arguments

df

A VCF as a data frame / data.table with columns CHROM, POS, ALT.

ref_genome

A BSgenome object or a character identifier accepted by normalize_genome_arg().

trans_ranges

Optional data.table of transcript ranges with columns chrom, start, end, strand, Ensembl.gene.ID, gene.symbol. If NULL, the shipped table for ref_genome is used.

name_of_vcf

Optional VCF name used in warning/error messages.

Value

A data.table with the annotation columns added (left-join semantics: variants outside any transcript have NA values).

Details

If trans_ranges is NULL and no shipped table is available for the given ref_genome, returns df as a data.table unchanged (no strand columns added). If df has zero rows, it is returned unchanged.