SNPlocs-class {BSgenome} | R Documentation

## SNPlocs objects

### Description

The SNPlocs class is a container for storing known SNP locations (of class snp) for a given organism.

SNPlocs objects are usually made in advance by a volunteer and made available to the Bioconductor community as SNPlocs data packages. See `?available.SNPs` for how to get the list of SNPlocs and XtraSNPlocs data packages curently available.

The main focus of this man page is on how to extract SNPs from an SNPlocs object.

### Usage

    snpcount(x)

    snpsBySeqname(x, seqnames, ...)
    ## S4 method for signature 'SNPlocs'
    snpsBySeqname(x, seqnames, drop.rs.prefix=FALSE)

    snpsByOverlaps(x, ranges, ...)
    ## S4 method for signature 'SNPlocs'
    snpsByOverlaps(x, ranges, drop.rs.prefix=FALSE, ...)

    snpsById(x, ids, ...)
    ## S4 method for signature 'SNPlocs'
    snpsById(x, ids, ifnotfound=c("error", "warning", "drop"))

### Arguments

`x` | A SNPlocs object.
`seqnames` | The names of the sequences for which to get SNPs. Must be a subset of `seqlevels(x)`. NAs and duplicates are not allowed.
`...` | Additional arguments, for use in specific methods. Arguments passed to the `snpsByOverlaps` method for SNPlocs objects thru `...` are used internally in the call to `subsetByOverlaps()`. See `?IRanges::subsetByOverlaps` in the IRanges package and `?GenomicRanges::subsetByOverlaps` in the GenomicRanges package for more information about the `subsetByOverlaps()` generic and its method for GenomicRanges objects.
`drop.rs.prefix` | Should the `rs` prefix be dropped from the returned RefSNP ids? (RefSNP ids are stored in the `RefSNP_id` metadata column of the returned object.)
`ranges` | One or more genomic regions of interest specified as a GRanges or GPos object. A single region of interest can be specified as a character string of the form `"ch14:5201-5300"`.
`ids` | The RefSNP ids to look up (a.k.a. rs ids). Can be integer or character vector, with or without the `"rs"` prefix. NAs are not allowed.
`ifnotfound` | What to do if SNP ids are not found.

### Value

`snpcount` returns a named integer vector containing the number of SNPs for each sequence in the reference genome.

`snpsBySeqname`, `snpsByOverlaps`, and `snpsById` return an unstranded GPos object with 1 element (genomic position) per SNP and the following metadata columns:

- `RefSNP_id`: RefSNP ID (aka "rs id"). Character vector with no NAs and no duplicates.

- `alleles_as_ambig`: A character vector with no NAs containing the alleles for each SNP represented by an IUPAC nucleotide ambiguity code. See `?IUPAC_CODE_MAP` in the Biostrings package for more information. The alleles are always reported with respect to the positive strand.

Note that this GPos object is unstranded i.e. all the SNPs in it have their strand set to `"*"`.

If `ifnotfound="error"`, the object returned by `snpsById` is guaranteed to be parallel to `ids`, that is, the i-th element in the GPos object corresponds to the i-th element in `ids`.

### Author(s)

H. Pagès

### See Also

- `available.SNPs`

- GPos and GRanges objects in the GenomicRanges package.

- XtraSNPlocs packages and objects for molecular variations of class other than snp e.g. of class in-del, heterozygous, microsatellite, etc...

- `IRanges::subsetByOverlaps` in the IRanges package and `GenomicRanges::subsetByOverlaps` in the GenomicRanges package for more information about the `subsetByOverlaps()` generic and its method for GenomicRanges objects.

- `injectSNPs`

- `IUPAC_CODE_MAP` in the Biostrings package.

### Examples

    library(SNPlocs.Hsapiens.dbSNP144.GRCh38)
    snps <- SNPlocs.Hsapiens.dbSNP144.GRCh38
    snpcount(snps)

    ## ---------------------------------------------------------------------
    ## snpsBySeqname()
    ## ---------------------------------------------------------------------

    ## Get all SNPs located on chromosome 22 or MT:
    snpsBySeqname(snps, c("22", "MT"))

    ## ---------------------------------------------------------------------
    ## snpsByOverlaps()
    ## ---------------------------------------------------------------------

    ## Get all SNPs overlapping some genomic region of interest:
    snpsByOverlaps(snps, "22:33.63e6-33.64e6")

    ## With the regions of interest being all the known CDS for hg38
    ## located on chromosome 22 or MT (except for the chromosome naming
    ## convention, hg38 is the same as GRCh38):
    library(TxDb.Hsapiens.UCSC.hg38.knownGene)
    txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
    my_cds <- cds(txdb)
    seqlevels(my_cds, pruning.mode="coarse") <- c("chr22", "chrM")
    seqlevelsStyle(my_cds)  # UCSC
    seqlevelsStyle(snps)    # NCBI
    seqlevelsStyle(my_cds) <- seqlevelsStyle(snps)
    genome(my_cds) <- genome(snps)
    my_snps <- snpsByOverlaps(snps, my_cds)
    my_snps
    table(my_snps %within% my_cds)

    ## ---------------------------------------------------------------------
    ## snpsById()
    ## ---------------------------------------------------------------------

    ## Lookup some RefSNP ids:
    my_rsids <- c("rs10458597", "rs12565286", "rs7553394")
    ## Not run:
      snpsById(snps, my_rsids)  # error, rs7553394 not found

    ## End(Not run)
    ## The following example uses more than 2GB of memory, which is more
    ## than what 32-bit Windows can handle:
    is_32bit_windows <- .Platform$OS.type == "windows" &&
                        .Platform$r_arch == "i386"
    if (!is_32bit_windows) {
        snpsById(snps, my_rsids, ifnotfound="drop")
    }

[Package BSgenome version 1.52.0 Index]