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LDlinkR: Calculating Linkage Disequilibrium (LD) in Human

8 août 2022 Package 'LDlinkR'. August 8 2022. Type Package. Title Calculating Linkage Disequilibrium (LD) in Human Population. Groups of Interest.



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  • How do I find all SNPs in LD?

    "to obtain all LD values from a group of SNPs with other SNPs, use the command --ld-snp-list mysnps. txt where mysnps. txt is a list of SNPs."

  • How do you calculate LD decay?

    The LD decay was determined by plotting the r2 values against the genetic distance of loci pairs (Mb) for each chromosome and a trend line describing the LD decay was calculated by locally-weighted polynomial regression (LOESS) in R (http://www.r-project.org).

  • What is linkage disequilibrium LD analysis?

    Linkage disequilibrium (LD) is a population-based parameter that describes the degree to which an allele of one genetic variant is inherited or correlated with an allele of a nearby genetic variant within a given population (Bush and Moore, 2012).
  • LD is of importance in evolutionary biology and human genetics because so many factors affect it and are affected by it. LD provides information about past events and it constrains the potential response to both natural and artificial selection.

Package 'LDlinkR"

May 31, 2023

TypePackage

TitleCalculating Linkage Disequilibrium (LD) in Human Population

Groups of Interest

Version1.3.0

MaintainerTimothy A. Myers

DescriptionProvides access to the "LDlink" API () using the R console. This programmatic access facilitates researchers who are interested in perform- ing batch queries in 1000 Genomes Project (2015) < doi:10.1038/nature15393 data using "LDlink". "LDlink" is an interactive and powerful suite of web-based tools for querying germline variants in human population groups of interest. For more details, please see

Machiela et al. (2015) <

doi:10.1093/bioinformatics/btv402

LicenseGPL (>= 2)

URLhttps://ldlink.nih.gov

EncodingUTF-8

Importshttr (>= 1.4.0), utils (>= 3.4.2)

Suggeststestthat, knitr, rmarkdown, spelling

VignetteBuilderknitr

RoxygenNote7.2.3

Languageen-US

NeedsCompilationno

AuthorTimothy A. Myers [aut, cre] (),

Stephen J. Chanock [aut],

Mitchell J. Machiela [aut] ()

RepositoryCRAN

Date/Publication2023-05-31 18:10:02 UTC

1

2LDexpress

Rtopics documented:

LDexpress . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 LDhap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 LDmatrix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 LDpair . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 LDpop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 LDproxy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 LDproxy_batch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 LDtrait . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 list_chips . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 list_gtex_tissues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 list_pop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 SNPchip . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 SNPclip . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 Index16LDexpressDetermine if genomic variants are associated with gene expression.Description Search if a list of genomic variants (or variants in LD with those variants) is associated with gene expression in tissues of interest. Quantitative trait loci data is downloaded from the GTEx Portal (https://gtexportal.org/home/). Usage

LDexpress(

snps, pop = "CEU", tissue = "ALL", r2d = "r2", r2d_threshold = 0.1, p_threshold = 0.1, win_size = 5e+05, genome_build = "grch37", token = NULL, file = FALSE, api_root = "https://ldlink.nih.gov/LDlinkRest"

Arguments

snpsbetween1-10variants, usinganrsIDorchromosomecoordinate(e.g. "chr7:24966446")

LDexpress3

popa 1000 Genomes Project population, (e.g. YRI or CEU), multiple allowed, de- fault = "CEU". Use the 'list_pop' function to see a list of available human reference populations. tissueselectfrom1-54non-diseasedtissuesitescollectedfortheGTExproject, multi- pleallowed. Acceptableuserinput istakeneither from"tissue_name_ldexpress" or "tissue_abbrev_ldexpress" (tissue abbreviation) code listed in available GTEx tissue sites using thelist_getex_tissues()function (e.g. "ADI_SUB" for Adipose Subcutaneous). Input is case sensitive. Default = "ALL" for all avail- able tissue types. r2deither "r2" for LD R2 or "d" for LD D", default = "r2". r2d_thresholdR2 or D" (depends on "r2d" user input parameter) threshold for LD filtering. Any variants within -/+ of the specified genomic window and R^2 or D" less than the threshold will be removed. Value needs to be in the range 0 to 1. Default value is 0.1. p_thresholddefine the eQTL significance threshold used for returning query results. Default value is 0.1 which returns all GTEx eQTL associations with P-value less than 0.1. win_sizeset genomic window size for LD calculation. Specify a value greater than or equal to zero and less than or equal to 1,000,000 basepairs (bp). Default value is -/+ 500,000bp. genome_buildChoose between one of the three options...'grch37' for genome build GRCh37 (hg19), 'grch38' for GRCh38 (hg38), or 'grch38_high_coverage' for GRCh38 High Coverage (hg38) 1000 Genome Project data sets. Default is GRCh37 (hg19). tokenLDlink provided user token, default = NULL, register for token athttps:// ldlink.nih.gov/?tab=apiaccess fileOptional character string naming a path and file for saving results. If file = FALSE, no file will be generated, default = FALSE. api_rootOptional alternative root url for API. Value A data frame of all query variant RS numbers, respective QTL which are in LD with query variant, and associated gene expression.

Examples

## Not run: LDexpress(snps = c("rs345", "rs456"), pop = c("YRI", "CEU"), tissue = c("ADI_SUB", "ADI_VIS_OME"), r2d = "r2", r2d_threshold = "0.1", p_threshold = "0.1", win_size = "500000", genome_build = "grch37", token = Sys.getenv("LDLINK_TOKEN")

4LDhap

## End(Not run)LDhapCalculates population specific haplotype frequencies of all haplotypes observed for a list of query variants.Description Calculates population specific haplotype frequencies of all haplotypes observed for a list of query variants. Usage

LDhap(

snps, pop = "CEU", token = NULL, file = FALSE, table_type = "haplotype", genome_build = "grch37", api_root = "https://ldlink.nih.gov/LDlinkRest"

Arguments

snpslist of between 1 - 30 variants, using an rsID or chromosome coordinate (e.g. "chr7:24966446") popa 1000 Genomes Project population, (e.g. YRI or CEU), multiple allowed, de- fault = "CEU" tokenLDlink provided user token, default = NULL, register for token athttps:// ldlink.nih.gov/?tab=apiaccess fileOptional character string naming a path and file for saving results. If file = FALSE, no file will be generated, default = FALSE. 'variant', 'both' and 'merged'. Default = "haplotype". genome_buildChoose between one of the three options...'grch37' for genome build GRCh37 (hg19), 'grch38' for GRCh38 (hg38), or 'grch38_high_coverage' for GRCh38 High Coverage (hg38) 1000 Genome Project data sets. Default is GRCh37 (hg19). api_rootOptional alternative root url for API. Value a data frame or list

LDmatrix5

Examples

## Not run: LDhap(c("rs3", "rs4", "rs148890987"), "CEU", token = Sys.getenv("LDLINK_TOKEN"))

## Not run: LDhap("rs148890987", c("YRI", "CEU"), token = Sys.getenv("LDLINK_TOKEN"))LDmatrixGenerates a data frame of pairwise linkage disequilibrium statistics.Description

Generates a data frame of pairwise linkage disequilibrium statistics. Usage

LDmatrix(

snps, pop = "CEU", r2d = "r2", token = NULL, file = FALSE, genome_build = "grch37", api_root = "https://ldlink.nih.gov/LDlinkRest"

Arguments

snpslist of between 2 - 1,000 variants, using an rsID or chromosome coordinate (e.g. "chr7:24966446") popa 1000 Genomes Project population, (e.g. YRI or CEU), multiple allowed, de- fault = "CEU" r2dr2d, either "r2" for LD R2 or "d" for LD D", default = "r2" tokenLDlink provided user token, default = NULL, register for token athttps:// ldlink.nih.gov/?tab=apiaccess fileOptional character string naming a path and file for saving results. If file = FALSE, no file will be generated, default = FALSE. genome_buildChoose between one of the three options...'grch37' for genome build GRCh37 (hg19), 'grch38' for GRCh38 (hg38), or 'grch38_high_coverage' for GRCh38 High Coverage (hg38) 1000 Genome Project data sets. Default is GRCh37 (hg19). api_rootOptional alternative root url for API. Value a data frame

6LDpair

Examples

## Not run: LDmatrix(c("rs3", "rs4", "rs148890987"), "YRI", "r2", token = Sys.getenv("LDLINK_TOKEN")) ## End(Not run)LDpairInvestigates potentially correlated alleles for a pair of variants.Description Investigates potentially correlated alleles for a pair of variants. Usage

LDpair(

var1, var2, pop = "CEU", token = NULL, output = "table", file = FALSE, genome_build = "grch37", api_root = "https://ldlink.nih.gov/LDlinkRest"

Arguments

var1the first RS number or genomic coordinate (e.g. "chr7:24966446") var2the second RS number or genomic coordinate (e.g. "ch7:24966446") popa 1000 Genomes Project population(s), (e.g. YRI or CEU), multiple allowed, default = "CEU" tokenLDlink provided user token, default = NULL, register for token athttps:// ldlink.nih.gov/?tab=apiaccess outputtwo output options available, "text", which displays a two-by-two matrix dis- playing haplotype counts and allele frequencies along with other statistics, or "table", which displays the same data in rows and columns, default = "table" fileOptional character string naming a path and file for saving results. If file = FALSE, no file will be generated, default = FALSE. genome_buildChoose between one of the three options...'grch37' for genome build GRCh37 (hg19), 'grch38' for GRCh38 (hg38), or 'grch38_high_coverage' for GRCh38 High Coverage (hg38) 1000 Genome Project data sets. Default is GRCh37 (hg19). api_rootOptional alternative root url for API.

LDpop7

Value text or data frame, depending on the output option

Examples

## Not run: LDpair(var1 = "rs3", var2 = "rs4", pop = "YRI", token = Sys.getenv("LDLINK_TOKEN"))

## Not run: LDpair("rs3", "rs4", "YRI", token = Sys.getenv("LDLINK_TOKEN"), "text")LDpopInvestigates allele frequencies and linkage disequilibrium patterns

across 1000 Genomes Project populations.Description Investigates allele frequencies and linkage disequilibrium patterns across 1000 Genomes Project populations. Usage

LDpop(

var1, var2, pop = "CEU", r2d = "r2", token = NULL, file = FALSE, genome_build = "grch37", api_root = "https://ldlink.nih.gov/LDlinkRest"

Arguments

var1the first RS number or genomic coordinate (e.g. "chr7:24966446") var2the second RS number or genomic coordinate (e.g. "ch7:24966446") popa 1000 Genomes Project population(s), (e.g. YRI or CEU), multiple allowed, default = "CEU" r2deither "r2" for LD R2 or "d" for LD D", default = "r2" tokenLDlink provided user token, default = NULL, register for token athttps:// ldlink.nih.gov/?tab=apiaccess fileOptional character string naming a path and file for saving results. If file = FALSE, no file will be generated, default = FALSE. genome_buildChoose between one of the three options...'grch37' for genome build GRCh37 (hg19), 'grch38' for GRCh38 (hg38), or 'grch38_high_coverage' for GRCh38 High Coverage (hg38) 1000 Genome Project data sets. Default is GRCh37 (hg19). api_rootOptional alternative root url for API.

8LDproxy

Value a data frame

Examples

## Not run: LDpop(var1 = "rs3", var2 = "rs4", pop = "YRI", r2d = "r2", token = Sys.getenv("LDLINK_TOKEN")) ## End(Not run)LDproxyExplore proxy and putative functional variants for a single query vari- ant.Description Explore proxy and putative functional variants for a single query variant. Usage

LDproxy(

snp, pop = "CEU", r2d = "r2", token = NULL, file = FALSE, genome_build = "grch37", api_root = "https://ldlink.nih.gov/LDlinkRest"

Arguments

snpan rsID or chromosome coordinate (e.g. "chr7:24966446"), one per query popa 1000 Genomes Project population, (e.g. YRI or CEU), multiple allowed, de- fault = "CEU" r2deither "r2" for LD R2 or "d" for LD D", default = "r2" tokenLDlink provided user token, default = NULL, register for token athttps:// ldlink.nih.gov/?tab=apiaccess fileOptional character string naming a path and file for saving results. If file = FALSE, no file will be generated, default = FALSE. genome_buildChoose between one of the three options...'grch37' for genome build GRCh37 (hg19), 'grch38' for GRCh38 (hg38), or 'grch38_high_coverage' for GRCh38 High Coverage (hg38) 1000 Genome Project data sets. Default is GRCh37 (hg19). api_rootOptional alternative root url for API.

LDproxy_batch9

Value a data frame

Examples

## Not run: LDproxy("rs456", "YRI", "r2", token = Sys.getenv("LDLINK_TOKEN"))LDproxy_batchQuery LDproxy using a list of query variants, one per line.Description

Query LDproxy using a list of query variants, one per line. Usage

LDproxy_batch(

snp, pop = "CEU", r2d = "r2", token = NULL, append = FALSE, genome_build = "grch37", api_root = "https://ldlink.nih.gov/LDlinkRest"

Arguments

snpa character string or data frame listing rsID"s or chromosome coordinates (e.g. "chr7:24966446"), one per linequotesdbs_dbs17.pdfusesText_23
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