Last data update: 2014.03.03

 R: XtraSNPlocs objects
XtraSNPlocs-classR Documentation

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.

This man page's main focus is on how to extract data 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, maxgap=0L, minoverlap=0L,
               type=c("any", "start", "end", "within", "equal"),
               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".

maxgap, minoverlap, type

These arguments are passed to subsetByOverlaps() which is used internally by snpsByOverlaps. 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.

...

Additional arguments, for use in specific methods. Further arguments passed to the snpsByOverlaps method for XtraSNPlocs objects (thru ...) are passed to subsetByOverlaps().

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. Pag<c3><83><c2><a8>s

See Also

  • available.SNPs

  • SNPlocs objects.

Examples

library(XtraSNPlocs.Hsapiens.dbSNP141.GRCh38)
snps <- XtraSNPlocs.Hsapiens.dbSNP141.GRCh38
snpcount(snps)
colnames(snps)

## ---------------------------------------------------------------------
## snpsBySeqname()
## ---------------------------------------------------------------------
## Get the location, RefSNP id, and alleles for all "extra SNPs"
## located on chromosome 22 and 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.dbSNP141.GRCh38 for examples of using
## snpsBySeqname() and snpsById().

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(BSgenome)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/BSgenome/XtraSNPlocs-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: XtraSNPlocs-class
> ### Title: XtraSNPlocs objects
> ### Aliases: class:XtraSNPlocs XtraSNPlocs-class XtraSNPlocs
> ###   colnames,XtraSNPlocs-method dim,XtraSNPlocs-method
> ###   provider,XtraSNPlocs-method providerVersion,XtraSNPlocs-method
> ###   releaseDate,XtraSNPlocs-method releaseName,XtraSNPlocs-method
> ###   referenceGenome,XtraSNPlocs-method organism,XtraSNPlocs-method
> ###   commonName,XtraSNPlocs-method species,XtraSNPlocs-method
> ###   seqinfo,XtraSNPlocs-method seqnames,XtraSNPlocs-method newXtraSNPlocs
> ###   show,XtraSNPlocs-method snpcount,XtraSNPlocs-method
> ###   snpsBySeqname,XtraSNPlocs-method snpsByOverlaps,XtraSNPlocs-method
> ###   snpsById,XtraSNPlocs-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
> library(XtraSNPlocs.Hsapiens.dbSNP141.GRCh38)
> snps <- XtraSNPlocs.Hsapiens.dbSNP141.GRCh38
> snpcount(snps)
   ch1    ch2    ch3    ch4    ch5    ch6    ch7    ch8    ch9   ch10   ch11 
546378 584439 464593 456879 411943 471931 379787 332813 277342 327169 315134 
  ch12   ch13   ch14   ch15   ch16   ch17   ch18   ch19   ch20   ch21   ch22 
327687 238349 215014 199033 199383 202858 184432 167132 153060 100948  94680 
   chX    chY   chMT 
226135  10298     46 
> colnames(snps)
[1] "seqnames"  "start"     "end"       "width"     "strand"    "RefSNP_id"
[7] "alleles"   "snpClass"  "loctype"  
> 
> ## ---------------------------------------------------------------------
> ## snpsBySeqname()
> ## ---------------------------------------------------------------------
> ## Get the location, RefSNP id, and alleles for all "extra SNPs"
> ## located on chromosome 22 and MT:
> snpsBySeqname(snps, c("ch22", "chMT"), columns=c("RefSNP_id", "alleles"))
GRanges object with 94726 ranges and 2 metadata columns:
          seqnames               ranges strand |   RefSNP_id     alleles
             <Rle>            <IRanges>  <Rle> | <character> <character>
      [1]     ch22 [10513380, 10513380]      - | rs386831164         -/T
      [2]     ch22 [10519678, 10519677]      + |  rs71286731       -/TTT
      [3]     ch22 [10526387, 10526386]      + |  rs36149894         -/A
      [4]     ch22 [10547411, 10547413]      + |   rs4022899       -/TTA
      [5]     ch22 [10551396, 10551396]      - |  rs67003614         -/T
      ...      ...                  ...    ... .         ...         ...
  [94722]     chMT       [16180, 16181]      + | rs371240719        -/AA
  [94723]     chMT       [16187, 16189]      + | rs386828865 CCT/TCC/TGC
  [94724]     chMT       [16189, 16189]      + | rs369574569        CC/T
  [94725]     chMT       [16291, 16292]      + | rs386828866       CC/TT
  [94726]     chMT       [16293, 16294]      + | rs386828867    AC/GT/TT
  -------
  seqinfo: 25 sequences (1 circular) from GRCh38 genome
> 
> ## ---------------------------------------------------------------------
> ## 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"))
GRanges object with 32 ranges and 2 metadata columns:
       seqnames               ranges strand |   RefSNP_id     alleles
          <Rle>            <IRanges>  <Rle> | <character> <character>
   [1]     ch22 [33630832, 33630832]      + |  rs11366195         -/A
   [2]     ch22 [33631155, 33631158]      + | rs113414007      -/CTGT
   [3]     ch22 [33631157, 33631160]      + |  rs61016685      -/GTCT
   [4]     ch22 [33631157, 33631161]      + | rs201902868     -/GTCTA
   [5]     ch22 [33631162, 33631162]      + | rs376379301         -/T
   ...      ...                  ...    ... .         ...         ...
  [28]     ch22 [33637609, 33637608]      + |   rs3831697     -/CC/CT
  [29]     ch22 [33638237, 33638241]      + | rs375674091     -/AAGGT
  [30]     ch22 [33638460, 33638459]      + | rs147043500      -/ATTA
  [31]     ch22 [33638463, 33638462]      + |  rs10689394      -/ATTA
  [32]     ch22 [33638464, 33638463]      + |  rs67593517      -/ATTA
  -------
  seqinfo: 25 sequences (1 circular) from GRCh38 genome
> 
> ## 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)
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
> hg38_cds <- cds(txdb)
> seqlevelsStyle(hg38_cds)  # UCSC
[1] "UCSC"
> seqlevelsStyle(snps)  # dbSNP
[1] "dbSNP"
> seqlevelsStyle(hg38_cds) <- seqlevelsStyle(snps)
> genome(hg38_cds) <- genome(snps)
> snpsByOverlaps(snps, hg38_cds, columns=c("RefSNP_id", "alleles"))
GRanges object with 21511 ranges and 2 metadata columns:
          seqnames                 ranges strand |   RefSNP_id      alleles
             <Rle>              <IRanges>  <Rle> | <character>  <character>
      [1]      ch1       [939437, 939436]      + | rs200996316          -/T
      [2]      ch1       [946527, 946526]      - |  rs34516061          -/G
      [3]      ch1       [965122, 965121]      + | rs140189896  -/GGGGGGGGG
      [4]      ch1       [966539, 966538]      + | rs371900006          -/C
      [5]      ch1       [966592, 966591]      + | rs372692701          -/T
      ...      ...                    ...    ... .         ...          ...
  [21507]      chX [155033410, 155033410]      + |  rs35561365          -/T
  [21508]      chX [155033422, 155033422]      + |  rs36000410          -/T
  [21509]      chX [155033446, 155033446]      + |  rs35784904          -/T
  [21510]      chX [155090809, 155090818]      + | rs267606404 -/TCCAATCCAT
  [21511]      chY [ 19587278,  19587279]      + | rs372084928         -/CT
  -------
  seqinfo: 25 sequences (1 circular) from GRCh38 genome
> 
> ## ---------------------------------------------------------------------
> ## 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"))
GRanges object with 7 ranges and 2 metadata columns:
      seqnames                 ranges strand |   RefSNP_id     alleles
         <Rle>              <IRanges>  <Rle> | <character> <character>
  [1]      ch7 [148586457, 148586460]      + | rs367617508      -/ACAG
  [2]      ch2 [160890468, 160890467]      + | rs398104919         -/A
  [3]     ch22 [ 33637609,  33637608]      + |   rs3831697     -/CC/CT
  [4]      ch1 [ 93471610,  93471610]      + | rs372470289         -/T
  [5]     ch18 [ 43189986,  43189986]      + | rs141568169         -/A
  [6]     ch15 [ 45691525,  45691524]      + |  rs34628976         -/C
  [7]     ch14 [ 21488084,  21488083]      + |  rs67551854        -/AG
  -------
  seqinfo: 25 sequences (1 circular) from GRCh38 genome
> 
> ## See ?XtraSNPlocs.Hsapiens.dbSNP141.GRCh38 for examples of using
> ## snpsBySeqname() and snpsById().
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>


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