BSgenome: XtraSNPlocs-class – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

XtraSNPlocs-class

XtraSNPlocs objects

Description

The XtraSNPlocs class is a container for storing extra SNP locations and alleles for a given organism. While a SNPlocs object can store only molecular variations of class snp, an XtraSNPlocs object contains molecular variations of other classes (in-del, heterozygous, microsatellite, named-locus, no-variation, mixed, multinucleotide-polymorphism).

XtraSNPlocs objects are usually made in advance by a volunteer and made available to the Bioconductor community as XtraSNPlocs 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 XtraSNPlocs object.

Usage

## S4 method for signature 'XtraSNPlocs'
snpcount(x)

## S4 method for signature 'XtraSNPlocs'
snpsBySeqname(x, seqnames,
        columns=c("seqnames", "start", "end", "strand", "RefSNP_id"),
        drop.rs.prefix=FALSE, as.DataFrame=FALSE)

## S4 method for signature 'XtraSNPlocs'
snpsByOverlaps(x, ranges,
        columns=c("seqnames", "start", "end", "strand", "RefSNP_id"),
        drop.rs.prefix=FALSE, as.DataFrame=FALSE, ...)

## S4 method for signature 'XtraSNPlocs'
snpsById(x, ids,
        columns=c("seqnames", "start", "end", "strand", "RefSNP_id"),
        ifnotfound=c("error", "warning", "drop"), as.DataFrame=FALSE)

## S4 method for signature 'XtraSNPlocs'
colnames(x, do.NULL=TRUE, prefix="col")

Arguments

`x`	An XtraSNPlocs object.
`seqnames`	The names of the sequences for which to get SNPs. NAs and duplicates are not allowed. The supplied `seqnames` must be a subset of `seqlevels(x)`.
`columns`	The names of the columns to return. Valid column names are: `seqnames`, `start`, `end`, `width`, `strand`, `RefSNP_id`, `alleles`, `snpClass`, `loctype`. See Details section below for a description of these columns.
`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.)
`as.DataFrame`	Should the result be returned in a DataFrame instead of a GRanges object?
`ranges`	One or more regions of interest specified as a GRanges object. A single region of interest can be specified as a character string of the form `"ch14:5201-5300"`.
`...`	Additional arguments, for use in specific methods. Arguments passed to the `snpsByOverlaps` method for XtraSNPlocs 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.
`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.
`do.NULL, prefix`	These arguments are ignored.

Value

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

snpsBySeqname and snpsById both return a GRanges object with 1 element per SNP, unless as.DataFrame is set to TRUE in which case they return a DataFrame with 1 row per SNP. When a GRanges object is returned, the columns requested via the columns argument are stored as metada columns of the object, except for the following columns: seqnames, start, end, width, and strand. These "spatial columns" (in the sense that they describe the genomic locations of the SNPs) can be accessed by calling the corresponding getter on the GRanges object.

Summary of available columns (my_snps being the returned object):

seqnames: The name of the chromosome where each SNP is located. Access with seqnames(my_snps) when my_snps is a GRanges object.
start and end: The starting and ending coordinates of each SNP with respect to the chromosome indicated in seqnames. Coordinated are 1-based and with respect to the 5' end of the plus strand of the chromosome in the reference genome. Access with start(my_snps), end(my_snps), or ranges(my_snps) when my_snps is a GRanges object.
width: The number of nucleotides spanned by each SNP on the reference genome (e.g. a width of 0 means the SNP is an insertion). Access with width( my_snps) when my_snps is a GRanges object.
strand: The strand that the alleles of each SNP was reported to. Access with strand(my_snps) when my_snps is a GRanges object.
RefSNP_id: The RefSNP id (a.k.a. rs id) of each SNP. Access with mcols(my_snps)$RefSNP_id when my_snps is a GRanges object.
alleles: The alleles of each SNP in the format used by dbSNP. Access with mcols(my_snps)$alleles when my_snps is a GRanges object.
snpClass: Class of each SNP. Possible values are in-del, heterozygous, microsatellite, named-locus, no-variation, mixed, and multinucleotide-polymorphism. Access with mcols(my_snps)$snpClass when my_snps is a GRanges object.
loctype: See ftp://ftp.ncbi.nih.gov/snp/00readme.txt for the 6 loctype codes used by dbSNP, and their meanings. WARNING: The code assigned to each SNP doesn't seem to be reliable. For example, loctype codes 1 and 3 officially stand for insertion and deletion, respectively. However, when looking at the SNP ranges it actually seems to be the other way around. Access with mcols(my_snps)$loctype when my_snps is a GRanges object.

colnames(x) returns the names of the available columns.

Author(s)

H. Pagès

Examples

library(XtraSNPlocs.Hsapiens.dbSNP144.GRCh38)
snps <- XtraSNPlocs.Hsapiens.dbSNP144.GRCh38
snpcount(snps)
colnames(snps)

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

## Get the location, RefSNP id, and alleles for all "extra SNPs"
## located on chromosome 22 or MT:
snpsBySeqname(snps, c("ch22", "chMT"), columns=c("RefSNP_id", "alleles"))

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

## Get the location, RefSNP id, and alleles for all "extra SNPs"
## overlapping some regions of interest:
snpsByOverlaps(snps, "ch22:33.63e6-33.64e6",
               columns=c("RefSNP_id", "alleles"))

## With the regions of interest being all the known CDS for hg38
## (except for the chromosome naming convention, hg38 is the same
## as GRCh38):
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
hg38_cds <- cds(txdb)
seqlevelsStyle(hg38_cds)  # UCSC
seqlevelsStyle(snps)      # dbSNP
seqlevelsStyle(hg38_cds) <- seqlevelsStyle(snps)
genome(hg38_cds) <- genome(snps)
snpsByOverlaps(snps, hg38_cds, columns=c("RefSNP_id", "alleles"))

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

## Get the location and alleles for some RefSNP ids:
my_rsids <- c("rs367617508", "rs398104919", "rs3831697", "rs372470289",
              "rs141568169", "rs34628976", "rs67551854")
snpsById(snps, my_rsids, c("RefSNP_id", "alleles"))

## See ?XtraSNPlocs.Hsapiens.dbSNP144.GRCh38 for more examples of using
## snpsBySeqname() and snpsById().

BSgenome

Software infrastructure for efficient representation of full genomes and their SNPs

v1.58.0

Artistic-2.0

Authors

Hervé Pagès

Initial release