,
Stephen J. Chanock [aut],
Mitchell J. Machiela [aut] | Title: | Calculating Linkage Disequilibrium (LD) in Human Population Groups of Interest |
|---|---|
| Description: | Provides access to the 'LDlink' API (<https://ldlink.nih.gov/?tab=apiaccess>) using the R console. This programmatic access facilitates researchers who are interested in performing 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>. |
| Authors: | Timothy A. Myers [aut, cre] ,
Stephen J. Chanock [aut],
Mitchell J. Machiela [aut] |
| Maintainer: | Timothy A. Myers <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 1.4.0.9000 |
| Built: | 2024-11-12 05:41:50 UTC |
| Source: | https://github.com/cbiit/ldlinkr |
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/).
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" )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" )
snps |
between 1 - 10 variants, using an rsID or chromosome coordinate (e.g. "chr7:24966446") |
pop |
a 1000 Genomes Project population, (e.g. YRI or CEU), multiple allowed, default = "CEU". Use the 'list_pop' function to see a list of available human reference populations. |
tissue |
select from 1 - 54 non-diseased tissue sites collected for the GTEx project, multiple
allowed. Acceptable user input is taken either from "tissue_name_ldexpress" or "tissue_abbrev_ldexpress"
(tissue abbreviation) code listed in available GTEx tissue sites using the
|
r2d |
either "r2" for LD R2 or "d" for LD D', default = "r2". |
r2d_threshold |
R2 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_threshold |
define 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_size |
set 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_build |
Choose 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). |
token |
LDlink provided user token, default = NULL, register for token at https://ldlink.nih.gov/?tab=apiaccess |
file |
Optional character string naming a path and file for saving results. If file = FALSE, no file will be generated, default = FALSE. |
api_root |
Optional alternative root url for API. |
A data frame of all query variant RS numbers, respective QTL which are in LD with query variant, and associated gene expression.
## 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") ) ## End(Not run)## 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") ) ## End(Not run)
Calculates population specific haplotype frequencies of all haplotypes observed for a list of query variants.
LDhap( snps, pop = "CEU", token = NULL, file = FALSE, table_type = "haplotype", genome_build = "grch37", api_root = "https://ldlink.nih.gov/LDlinkRest" )LDhap( snps, pop = "CEU", token = NULL, file = FALSE, table_type = "haplotype", genome_build = "grch37", api_root = "https://ldlink.nih.gov/LDlinkRest" )
snps |
list of between 1 - 30 variants, using an rsID or chromosome coordinate (e.g. "chr7:24966446") |
pop |
a 1000 Genomes Project population, (e.g. YRI or CEU), multiple allowed, default = "CEU" |
token |
LDlink provided user token, default = NULL, register for token at https://ldlink.nih.gov/?tab=apiaccess |
file |
Optional character string naming a path and file for saving results. If file = FALSE, no file will be generated, default = FALSE. |
table_type |
Choose from one of four options available to determine output format type...'haplotype', 'variant', 'both' and 'merged'. Default = "haplotype". |
genome_build |
Choose 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_root |
Optional alternative root url for API. |
a data frame or list
## 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"))## 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"))
Generates a data frame of pairwise linkage disequilibrium statistics.
LDmatrix( snps, pop = "CEU", r2d = "r2", token = NULL, file = FALSE, genome_build = "grch37", api_root = "https://ldlink.nih.gov/LDlinkRest" )LDmatrix( snps, pop = "CEU", r2d = "r2", token = NULL, file = FALSE, genome_build = "grch37", api_root = "https://ldlink.nih.gov/LDlinkRest" )
snps |
list of between 2 - 2500 variants, using an rsID or chromosome coordinate (e.g. "chr7:24966446") |
pop |
a 1000 Genomes Project population, (e.g. YRI or CEU), multiple allowed, default = "CEU" |
r2d |
r2d, either "r2" for LD R2 or "d" for LD D', default = "r2" |
token |
LDlink provided user token, default = NULL, register for token at https://ldlink.nih.gov/?tab=apiaccess |
file |
Optional character string naming a path and file for saving results. If file = FALSE, no file will be generated, default = FALSE. |
genome_build |
Choose 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_root |
Optional alternative root url for API. |
a data frame
## Not run: LDmatrix(c("rs3", "rs4", "rs148890987"), "YRI", "r2", token = Sys.getenv("LDLINK_TOKEN")) ## End(Not run)## Not run: LDmatrix(c("rs3", "rs4", "rs148890987"), "YRI", "r2", token = Sys.getenv("LDLINK_TOKEN")) ## End(Not run)
Investigates potentially correlated alleles for a pair of variants.
LDpair( var1, var2, pop = "CEU", token = NULL, output = "table", file = FALSE, genome_build = "grch37", api_root = "https://ldlink.nih.gov/LDlinkRest" )LDpair( var1, var2, pop = "CEU", token = NULL, output = "table", file = FALSE, genome_build = "grch37", api_root = "https://ldlink.nih.gov/LDlinkRest" )
var1 |
the first RS number or genomic coordinate (e.g. "chr7:24966446") |
var2 |
the second RS number or genomic coordinate (e.g. "ch7:24966446") |
pop |
a 1000 Genomes Project population(s), (e.g. YRI or CEU), multiple allowed, default = "CEU" |
token |
LDlink provided user token, default = NULL, register for token at https://ldlink.nih.gov/?tab=apiaccess |
output |
two output options available, "text", which displays a two-by-two matrix displaying haplotype counts and allele frequencies along with other statistics, or "table", which displays the same data in rows and columns, default = "table" |
file |
Optional character string naming a path and file for saving results. If file = FALSE, no file will be generated, default = FALSE. |
genome_build |
Choose 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_root |
Optional alternative root url for API. |
text or data frame, depending on the output option
## 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")## 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")
Investigates allele frequencies and linkage disequilibrium patterns across 1000 Genomes Project populations.
LDpop( var1, var2, pop = "CEU", r2d = "r2", token = NULL, file = FALSE, genome_build = "grch37", api_root = "https://ldlink.nih.gov/LDlinkRest" )LDpop( var1, var2, pop = "CEU", r2d = "r2", token = NULL, file = FALSE, genome_build = "grch37", api_root = "https://ldlink.nih.gov/LDlinkRest" )
var1 |
the first RS number or genomic coordinate (e.g. "chr7:24966446") |
var2 |
the second RS number or genomic coordinate (e.g. "ch7:24966446") |
pop |
a 1000 Genomes Project population(s), (e.g. YRI or CEU), multiple allowed, default = "CEU" |
r2d |
either "r2" for LD R2 or "d" for LD D', default = "r2" |
token |
LDlink provided user token, default = NULL, register for token at https://ldlink.nih.gov/?tab=apiaccess |
file |
Optional character string naming a path and file for saving results. If file = FALSE, no file will be generated, default = FALSE. |
genome_build |
Choose 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_root |
Optional alternative root url for API. |
a data frame
## Not run: LDpop(var1 = "rs3", var2 = "rs4", pop = "YRI", r2d = "r2", token = Sys.getenv("LDLINK_TOKEN")) ## End(Not run)## Not run: LDpop(var1 = "rs3", var2 = "rs4", pop = "YRI", r2d = "r2", token = Sys.getenv("LDLINK_TOKEN")) ## End(Not run)
Explore proxy and putative functional variants for a single query variant.
LDproxy( snp, pop = "CEU", r2d = "r2", token = NULL, file = FALSE, genome_build = "grch37", win_size = "500000", api_root = "https://ldlink.nih.gov/LDlinkRest" )LDproxy( snp, pop = "CEU", r2d = "r2", token = NULL, file = FALSE, genome_build = "grch37", win_size = "500000", api_root = "https://ldlink.nih.gov/LDlinkRest" )
snp |
an rsID or chromosome coordinate (e.g. "chr7:24966446"), one per query |
pop |
a 1000 Genomes Project population, (e.g. YRI or CEU), multiple allowed, default = "CEU" |
r2d |
either "r2" for LD R2 or "d" for LD D', default = "r2" |
token |
LDlink provided user token, default = NULL, register for token at https://ldlink.nih.gov/?tab=apiaccess |
file |
Optional character string naming a path and file for saving results. If file = FALSE, no file will be generated, default = FALSE. |
genome_build |
Choose 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). |
win_size |
set base pair (bp) window size. Specify a value greater than or equal to zero and less than or equal to 1,000,000bp. Default value is 500,000bp. |
api_root |
Optional alternative root url for API. |
a data frame
## Not run: LDproxy("rs456", "YRI", "r2", token = Sys.getenv("LDLINK_TOKEN"))## Not run: LDproxy("rs456", "YRI", "r2", token = Sys.getenv("LDLINK_TOKEN"))
Query LDproxy using a list of query variants, one per line.
LDproxy_batch( snp, pop = "CEU", r2d = "r2", token = NULL, append = FALSE, genome_build = "grch37", win_size = "500000", api_root = "https://ldlink.nih.gov/LDlinkRest" )LDproxy_batch( snp, pop = "CEU", r2d = "r2", token = NULL, append = FALSE, genome_build = "grch37", win_size = "500000", api_root = "https://ldlink.nih.gov/LDlinkRest" )
snp |
a character string or data frame listing rsID's or chromosome coordinates (e.g. "chr7:24966446"), one per line |
pop |
a 1000 Genomes Project population, (e.g. YRI or CEU), multiple allowed, default = "CEU" |
r2d |
either "r2" for LD R2 or "d" for LD D', default = "r2" |
token |
LDlink provided user token, default = NULL, register for token at https://ldlink.nih.gov/?tab=apiaccess |
append |
A logical. If TRUE, output for each query variant is appended to a text file. If FALSE, output of each query variant is saved in its own text file. Default is FALSE. |
genome_build |
Choose 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). |
win_size |
set base pair (bp) window size. Specify a value greater than or equal to zero and less than or equal to 1,000,000bp. Default value is 500,000bp. |
api_root |
Optional alternative root url for API. |
text file(s) are saved to the current working directory.
## Not run: snps_to_upload <- c("rs3", "rs4") ## Not run: LDproxy_batch(snp = snps_to_upload, token = Sys.getenv("LDLINK_TOKEN"), append = FALSE)## Not run: snps_to_upload <- c("rs3", "rs4") ## Not run: LDproxy_batch(snp = snps_to_upload, token = Sys.getenv("LDLINK_TOKEN"), append = FALSE)
Search if a list of variants (or variants in LD with those variants) have been previously associated with a trait or disease. Trait and disease data is updated nightly from the GWAS Catalog (https://www.ebi.ac.uk/gwas/docs/file-downloads.
LDtrait( snps, pop = "CEU", r2d = "r2", r2d_threshold = 0.1, win_size = 5e+05, token = NULL, file = FALSE, genome_build = "grch37", api_root = "https://ldlink.nih.gov/LDlinkRest" )LDtrait( snps, pop = "CEU", r2d = "r2", r2d_threshold = 0.1, win_size = 5e+05, token = NULL, file = FALSE, genome_build = "grch37", api_root = "https://ldlink.nih.gov/LDlinkRest" )
snps |
between 1 - 50 variants, using an rsID or chromosome coordinate (e.g. "chr7:24966446"). All input variants must match a bi-allelic variant. |
pop |
a 1000 Genomes Project population, (e.g. YRI or CEU), multiple allowed, default = "CEU". Use the 'list_pop' function to see a list of available human reference populations. |
r2d |
use "r2" to filter desired output from a threshold based on estimated LD R2 (R squared) or "d" for LD D' (D-prime), default = "r2". |
r2d_threshold |
R2 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. |
win_size |
set genomic window size for LD calculation. Specify a value greater than or equal to zero and less than or equal to 1,000,000bp. Default value is -/+ 500,000 bp. |
token |
LDlink provided user token, default = NULL, register for token at https://ldlink.nih.gov/?tab=apiaccess |
file |
Optional character string naming a path and file for saving results. If file = FALSE, no file will be generated, default = FALSE. |
genome_build |
Choose 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_root |
Optional alternative root url for API. |
A data frame of all query variant RS numbers with a list of queried variants in LD with a variant reported in the GWAS Catalog (https://www.ebi.ac.uk/gwas/docs/file-downloads.
## Not run: LDtrait(snps = "rs456", pop = c("YRI", "CEU"), r2d = "r2", r2d_threshold = "0.1", win_size = "500000", token = Sys.getenv("LDLINK_TOKEN") ) ## End(Not run)## Not run: LDtrait(snps = "rs456", pop = c("YRI", "CEU"), r2d = "r2", r2d_threshold = "0.1", win_size = "500000", token = Sys.getenv("LDLINK_TOKEN") ) ## End(Not run)
Provides a data frame listing the names and abbreviation codes for available commercial SNP Chip Arrays from Illumina and Affymetrix.
list_chips()list_chips()
a data frame listing the names and abbreviation codes for available SNP Chip Arrays from Illumina and Affymetrix
list_chips()list_chips()
Provides a data frame listing the GTEx full names, 'LDexpress' full names (without spaces) and acceptable abbreviation codes of the 54 non-diseased tissue sites collected for the GTEx Portal and used as input for the 'LDexpress' function.
list_gtex_tissues()list_gtex_tissues()
a data frame listing the GTEx tissues, their names and abbreviation codes used as input for LDexpress.
list_gtex_tissues()list_gtex_tissues()
Provides a data frame listing the available reference populations from the 1000 Genomes Project.
list_pop()list_pop()
a data frame listing the available reference populations, continental (ex: European, African, and Admixed American) and sub-populations (ex: Finnish, Gambian, and Peruvian)
list_pop()list_pop()
Find commercial genotyping chip arrays for variants of interest.
SNPchip( snps, chip = "ALL", token = NULL, file = FALSE, genome_build = "grch37", api_root = "https://ldlink.nih.gov/LDlinkRest" )SNPchip( snps, chip = "ALL", token = NULL, file = FALSE, genome_build = "grch37", api_root = "https://ldlink.nih.gov/LDlinkRest" )
snps |
between 1 - 5,000 variants, using an rsID or chromosome coordinate (e.g. "chr7:24966446") |
chip |
chip or arrays, platform code(s) for a SNP chip array, ALL_Illumina, ALL_Affy or ALL, default=ALL |
token |
LDlink provided user token, default = NULL, register for token at https://ldlink.nih.gov/?tab=apiaccess |
file |
Optional character string naming a path and file for saving results. If file = FALSE, no file will be generated, default = FALSE. |
genome_build |
Choose 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_root |
Optional alternative root url for API. |
a data frame
## Not run: SNPchip(c("rs3", "rs4", "rs148890987"), "ALL", token = Sys.getenv("LDLINK_TOKEN")) ## End(Not run) ## Not run: SNPchip(c("rs3", "rs4", "rs148890987"), c("A_CHB2", "A_SNP5.0"), token = Sys.getenv("LDLINK_TOKEN")) ## End(Not run) ## Not run: SNPchip("rs148890987", "ALL_Affy", token = Sys.getenv("LDLINK_TOKEN"))## Not run: SNPchip(c("rs3", "rs4", "rs148890987"), "ALL", token = Sys.getenv("LDLINK_TOKEN")) ## End(Not run) ## Not run: SNPchip(c("rs3", "rs4", "rs148890987"), c("A_CHB2", "A_SNP5.0"), token = Sys.getenv("LDLINK_TOKEN")) ## End(Not run) ## Not run: SNPchip("rs148890987", "ALL_Affy", token = Sys.getenv("LDLINK_TOKEN"))
Prune a list of variants by linkage disequilibrium.
SNPclip( snps, pop = "CEU", r2_threshold = "0.1", maf_threshold = "0.01", token = NULL, file = FALSE, genome_build = "grch37", api_root = "https://ldlink.nih.gov/LDlinkRest" )SNPclip( snps, pop = "CEU", r2_threshold = "0.1", maf_threshold = "0.01", token = NULL, file = FALSE, genome_build = "grch37", api_root = "https://ldlink.nih.gov/LDlinkRest" )
snps |
a list of between 1 - 5,000 variants, using an rsID or chromosome coordinate (e.g. "chr7:24966446") |
pop |
a 1000 Genomes Project population, (e.g. YRI or CEU), multiple allowed, default = "CEU" |
r2_threshold |
LD R2 threshold between 0-1, default = 0.1 |
maf_threshold |
minor allele frequency threshold between 0-1, default = 0.01 |
token |
LDlink provided user token, default = NULL, register for token at https://ldlink.nih.gov/?tab=apiaccess |
file |
Optional character string naming a path and file for saving results. If file = FALSE, no file will be generated, default = FALSE. |
genome_build |
Choose 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_root |
Optional alternative root url for API. |
a data frame
## Not run: SNPclip(c("rs3", "rs4", "rs148890987"), "YRI", "0.1", "0.01", token = Sys.getenv("LDLINK_TOKEN")) ## End(Not run)## Not run: SNPclip(c("rs3", "rs4", "rs148890987"), "YRI", "0.1", "0.01", token = Sys.getenv("LDLINK_TOKEN")) ## End(Not run)