Skip to contents

Annotate known SNP positions

Source: R/annot_rse.R
annot_snps.Rd

This function will annotate a GRanges or the rowRanges of a SummarizedExperiment with SNPs from a SNP package.

Usage

annot_snps(obj, ...)

# S3 method for class 'GRanges'
annot_snps(
  obj,
  dbsnp,
  chrom = NULL,
  col_to_aggr = "RefSNP_id",
  drop = FALSE,
  genome = NULL,
  RLE = TRUE,
  ...
)

# S3 method for class 'SummarizedExperiment'
annot_snps(obj, ...)

Arguments

obj

GRanges or SummarizedExperiment object

...

For the generic, further arguments to pass to specific methods. Unused for now.

dbsnp

SNPlocs package, see available packages from BSgenome::available.SNPs()

chrom

only operate on a specified chromosome

col_to_aggr

column from SNPlocs package to add to input. If multiple SNPs overlap these values will be concatenated as comma separated values.

drop

If TRUE, remove sites overlapping SNPs

genome

A BSgenome object, which if supplied, will be used to provide additional snp_ref_allele and snp_alt_alleles columns containing the reference and alt allele sequences, with respect to the positive strand. Additionally the snp sequences will be checked against the allele at the site if a column named ALT is present in object. The strand of the site will be used to determine if the ALT allele needs to be complemented prior to comparing against the SNP db (which always returns sequences w.r.t the plus strand).

RLE

If TRUE, columns added will returned as S4Vectors::Rle() vectors to reduce memory usage.

Value

Either a GRanges or SummarizedExperiment object with a new column added with information from col_to_aggr and optionally snp_ref_allele, snp_alt_alleles, and snp_matches_site annotations.

See also

SNPlocs.Hsapiens.dbSNP144.GRCh38

Examples

if (require(SNPlocs.Hsapiens.dbSNP144.GRCh38)) {
    gr <- GRanges(rep("22", 10),
        IRanges(
            seq(10510077,
                10610077,
                by = 1000
            )[1:10],
            width = 250
        ),
        strand = "+"
    )
    genome(gr) <- "GRCh38.p2"
    annot_snps(gr, SNPlocs.Hsapiens.dbSNP144.GRCh38)
}
#> Loading required package: SNPlocs.Hsapiens.dbSNP144.GRCh38
#> Loading required package: BSgenome
#> Loading required package: Biostrings
#> Loading required package: XVector
#> 
#> Attaching package: ‘Biostrings’
#> The following object is masked from ‘package:base’:
#> 
#>     strsplit
#> Loading required package: BiocIO
#> Loading required package: rtracklayer
#> 
#> Attaching package: ‘rtracklayer’
#> The following object is masked from ‘package:BiocIO’:
#> 
#>     FileForFormat
#> Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘SNPlocs.Hsapiens.dbSNP144.GRCh38’
#> GRanges object with 10 ranges and 1 metadata column:
#>        seqnames            ranges strand | RefSNP_id
#>           <Rle>         <IRanges>  <Rle> |     <Rle>
#>    [1]       22 10510077-10510326      + |          
#>    [2]       22 10511077-10511326      + | rs4022986
#>    [3]       22 10512077-10512326      + |          
#>    [4]       22 10513077-10513326      + |          
#>    [5]       22 10514077-10514326      + |          
#>    [6]       22 10515077-10515326      + |          
#>    [7]       22 10516077-10516326      + |          
#>    [8]       22 10517077-10517326      + |          
#>    [9]       22 10518077-10518326      + |          
#>   [10]       22 10519077-10519326      + |          
#>   -------
#>   seqinfo: 1 sequence from GRCh38.p2 genome; no seqlengths