Adds LD information to a 'locus' class object. It queries LDlink
(https://ldlink.nci.nih.gov/) via the LDlinkR package to retrieve linkage
disequilibrium (LD) information on a reference SNP.
link_LD(
loc,
pop = "CEU",
r2d = "r2",
token = "",
method = c("proxy", "matrix"),
genome_build = loc$genome,
...
)Returns a list object of class 'locus'. LD information is added as a
column ld in list element data.
Object of class 'locus' generated by locus()
A 1000 Genomes Project population, (e.g. YRI or CEU), multiple
allowed, default = "CEU". Passed to LDlinkR::LDmatrix().
Either "r2" for LD r^2 or "d" for LD D', default = "r2". Passed
to LDlinkR::LDmatrix() or LDproxy().
Personal access token for accessing 1000 Genomes LD data via
LDlink API. See LDlinkR package documentation.
Either "proxy" or "matrix". Controls whether to use
LDproxy() or LDmatrix() to obtain LD data.
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).
Optional arguments which are passed on to LDlinkR::LDmatrix() or
LDlinkR::LDproxy()
The argument method controls which LDlinkR function is used to retrieve LD
data. LDmatrix() is slower but usually more complete for small queries
(<1000 SNPs). However, it has a limit of 1000 SNPs which can be queried.
LDproxy() is faster but data on some SNPs may be absent.
Note, SNPs have to be correctly formatted as required by LDlinkR, either as
rsID (works with either method) or chromosome coordinate e.g. "chr7:24966446"
(works with LDproxy only). Default genome build is grch37, see LDproxy()
or LDmatrix().
locus()