Package 'ldblock'

c("\Sexpr[results=rd,stage=build]tools:::Rd_package_title(\"#1\")", "ldblock")data structures for linkage disequilibrium measures in populations

Description

c("\Sexpr[results=rd,stage=build]tools:::Rd_package_description(\"#1\")", "ldblock")Define data structures for linkage disequilibrium measures in populations.

Details

The DESCRIPTION file: c("\Sexpr[results=rd,stage=build]tools:::Rd_package_DESCRIPTION(\"#1\")", "ldblock")This package was not yet installed at build time.\cr c("\Sexpr[results=rd,stage=build]tools:::Rd_package_indices(\"#1\")", "ldblock") Index: This package was not yet installed at build time.\cr

Author(s)

c("\Sexpr[results=rd,stage=build]tools:::Rd_package_author(\"#1\")", "ldblock")VJ Carey <[email protected]>

Maintainer: c("\Sexpr[results=rd,stage=build]tools:::Rd_package_maintainer(\"#1\")", "ldblock")VJ Carey <[email protected]>

Examples

# see vignette

---

download hapmap resource with LD estimates

Description

download hapmap resource with LD estimates

Usage

downloadPopByChr(
  chrname = "chr1",
  popname = "CEU",
 
    urlTemplate = "http://hapmap.ncbi.nlm.nih.gov/downloads/ld_data/2009-02_phaseIII_r2/ld_%%CHRN%%_%%POPN%%.txt.gz",
  targfolder = Sys.getenv("LDBLOCK_TXTGZ_DIR")
)

Arguments

chrname	UCSC format tag for chromosome
popname	hapmap three letter code for population, e.g. 'CEU'
urlTemplate	pattern for creating URL given chr and pop
targfolder	destination

Details

delivers HapMap LD data to 'targfolder'

Value

just run for side effect of download.file

Examples

## Not run: 
 downloadPopByChr()
 
## End(Not run)

---

singletons from EUR

Description

singletons from EUR

Usage

EUR_singletons

Format

character vector

Source

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20130606_sample_info/20130606_sample_info.xlsx, to which superpopulation codes were added

---

Given a set of SNP identifiers, use LD to expand the set to include linked loci

Description

Given a set of SNP identifiers, use LD to expand the set to include linked loci

Usage

expandSnpSet(
  rsl,
  lb = 0.8,
  ldstruct,
  chrn = "chr17",
  popn = "CEU",
  txtgzfn = dir(system.file("hapmap", package = "ldblock"), full.names = TRUE)
)

Arguments

rsl	input list – SNPs not found in the LD structure are simply returned along with those found, and the expansion list, all combined in a vector
lb	lower bound on statistic used to retrieve loci in LD
ldstruct	instance of ldstruct-class
chrn	chromosome identifier
popn	population identifier (one of 'CEU', 'MEX', ...)
txtgzfn	path to gzipped hapmap file with LD information

Details

direct use of elementwise arithmetic comparison

Value

character vector

Note

As of 2015, it appears that locus names are more informative than addresses for determining SNP identity across resources.

Examples

og = Sys.getenv("LDBLOCK_TXTGZ_DIR")
  on.exit( Sys.setenv("LDBLOCK_TXTGZ_DIR" = og ) )
  Sys.setenv("LDBLOCK_TXTGZ_DIR"=system.file("hapmap", package="ldblock"))
  ld17 = hmld(chr="chr17", pop="CEU")
  ee = expandSnpSet( ld17@allrs[1:10], ldstruct = ld17 )

---

import hapmap LD data and create a structure for its management; generates a sparse matrix representation of pairwise LD statistics and binds metadata on variant name and position

Description

import hapmap LD data and create a structure for its management; generates a sparse matrix representation of pairwise LD statistics and binds metadata on variant name and position

Usage

hmld(hmgztxt, poptag, chrom, genome = "hg19", stat = "Dprime")

Arguments

hmgztxt	name of gzipped text file as distributed at hapmap.ncbi.nlm.nih.gov/downloads/ld_data/2009-02_phaseIII_r2/. It will be processed by read.delim.
poptag	heuristic tag identifying population
chrom	heuristic tag for chromosome name
genome	genome tag
stat	statistic to use, "Dprime", "R2", and "LOD" are options

Value

instance of ldstruct class

Examples

getClass("ldstruct")
# see vignette

---

Obtain LD statistics in region specified by a gene model.

Description

Obtain LD statistics in region specified by a gene model.

Usage

ldByGene(
  sym = "MMP24",
  vcf = system.file("vcf/c20exch.vcf.gz", package = "ldblock"),
  flank = 1000,
  vcfSLS = "NCBI",
  genomeSLS = "hg19",
  stats = "D.prime",
  depth = 10
)

Arguments

sym	A standard gene symbol for use with genemodel
vcf	Path to a tabix-indexed VCF file
flank	number of basepairs to flank gene model for search
vcfSLS	seqlevelsStyle (SLS) token for VCF; will be imposed on gene model
genomeSLS	character tag for genome, to be used with readVcf
stats	passed to ld
depth	passed to ld

Value

sparse matrix representation of selected LD statistic, as returned by ld

Note

Uses an internal function genemod4ldblock, that relies on EnsDb.Hsapiens.v75 to get gene model.

Examples

if (interactive()) {  # there is a warning owing to non-SNV present
ld1 = ldByGene(depth=150)
image(ld1[1:200,1:200], col.reg=heat.colors(120), colorkey=TRUE,
 main="SNPs in MMP24 (chr20)") 
}

---

use LDmat API from NCI LDlink service

Description

use LDmat API from NCI LDlink service

Usage

ldmat(rsvec, pop = "CEU", type = "d", token = Sys.getenv("LDLINK_TOKEN"))

Arguments

rsvec	character vector of SNP ids
pop	three letter code for HapMap population, defaults to CEU
type	'r2' or 'd', defaults to 'd' implying d-prime
token	the API token provided by NCI, defaults to value of environment variable LDLINK_TOKEN

Value

data.frame

Examples

if (interactive()) ldmat(c("rs77749396","rs9303279","rs9303280","rs9303281"))

---

accessor for matrix component

Description

accessor for matrix component

Usage

## S4 method for signature 'ldstruct'
ldmat(x)

Arguments

x	instance of ldstruct

---

container for LD data

Description

Manage information about LD statistics as reported by HapMap.

Objects from the Class

Objects can be created by calls of the form new("ldstruct", ...).

Examples

showClass("ldstruct")

---

Create a URL referencing 1000 genomes content in AWS S3. stack1kg produces a VcfStack instance with references to VCF for 1000 genomes autosomal chrs. S3-resident VCF files with version "v5a.20130502" are used.

Description

Create a URL referencing 1000 genomes content in AWS S3. stack1kg produces a VcfStack instance with references to VCF for 1000 genomes autosomal chrs. S3-resident VCF files with version "v5a.20130502" are used.

Usage

s3_1kg(chrnum, tmpl, dropchr = TRUE)

Arguments

chrnum	a character string denoting a chromosome, such as '22'
tmpl	alternate template for full URL, useful if versions prior to 2010 are of interest
dropchr	if TRUE chrnum will have 'chr' removed if present

Value

by default, a TabixFile instance

Note

The "wrap" parameter has been removed. A TabixFile structure will be returned. The tag parameter has been removed. Supply a tmpl argument if you are not using 20130502 version.

Examples

requireNamespace("Rsamtools")
s3_1kg("22") # try scanVcfHeader from VariantAnnotation

---

population and relationship information for 1000 genomes

Description

population and relationship information for 1000 genomes

Usage

sampinf_1kg

Format

data.frame

Source

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20130606_sample_info/20130606_sample_info.xlsx, to which superpopulation codes were added

---

couple together a group of VCFs

Description

couple together a group of VCFs

Usage

stack1kg(chrs = as.character(1:22), index = FALSE, useEBI = FALSE)

Arguments

chrs	a vector of chromosome names for extraction from 1000 genomes VCF collection
index	logical telling whether VcfStack should attempt to create the local index; for 1000 genomes, the tbi are in the cloud and will be used by readVcf so FALSE is appropriate
useEBI	logical(1) defaults to FALSE ... if TRUE, use tabix-indexed vcf from EBI, but in July 2022 the EBI FTP site does not respond. If FALSE, the AWS Open Data access path is used

Value

VcfStack instance

Note

The seqinfo component of returned stack will have NA for genome. Please set it manually; for useEBI=TRUE this would be GRCh38; very likely so for useEBI=FALSE, but this should be checked.

Examples

if (interactive()) {
  st1 = stack1kg()
  st1
  }

---