Package: ldblock 1.35.0

VJ Carey

ldblock: data structures for linkage disequilibrium measures in populations

Define data structures for linkage disequilibrium measures in populations.

# Install 'ldblock' in R:

install.packages('ldblock', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

On BioConductor:ldblock-1.35.0(bioc 3.20)ldblock-1.34.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

Last updated 2 months agofrom:ff2302759e

Vincent J. Carey, stvjc at channing.harvard.edu

Last update: 2020-06-30
Started: 2015-03-09

Help page	Topics
c("\Sexpr[results=rd,stage=build]tools:::Rd_package_title(\"#1\")", "ldblock")data structures for linkage disequilibrium measures in populations	ldblock-package ldblock
download hapmap resource with LD estimates	downloadPopByChr
singletons from EUR	EUR_singletons
Given a set of SNP identifiers, use LD to expand the set to include linked loci	expandSnpSet
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	hmld
Obtain LD statistics in region specified by a gene model.	ldByGene
use LDmat API from NCI LDlink service	ldmat
accessor for matrix component	ldmat,ldstruct-method
container for LD data	ldstruct-class
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.	s3_1kg
population and relationship information for 1000 genomes	sampinf_1kg
couple together a group of VCFs	stack1kg