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View Code? Open in Web Editor NEWLDlinkR: An R package for calculating linkage disequilibrium in human populations of interest
LDlinkR: An R package for calculating linkage disequilibrium in human populations of interest
Hello,
Recently I was pointed to your package, which I greatly appreciate. Unfortunately I've run into an issue:
I have SNP data in the format "chr"CHROM:POS, with positions ranging from 7 to 9 digits.
My data is from an imputation server that uses Genome Build 37.
However, LDlinkR only accepts positions of exactly 8 digits. What is the reason for that?
Furthermore, when appending the 7-digit positions with a 0 in front, I get no results either (example: "error: chr10:09062856 is not in dbSNP build 151.")
Thank you in advance.
When using LDproxy_batch(), if append = TRUE option, there's a warning message that the column headings are appended. In the output file, though, there is only on heading at the top, which is perfect.
There is a typo in the vignette that can result in an error. In the step where it asks you to set up the token, it uses LDLINKR_TOKEN but in the examples it uses LDLINK_TOKEN. It's missing the "R" from LDLINK.
Add PDF of extended examples as vignette
LDproxy_batch stops processing a list of SNPs when it encounters a variant that is not biallelic.
Hello,
I am really happy to see that this package exists, I have been using LDlink once in a while in the past years, and having some functions to do it easily with R without struggling with the request format and how to parse the output every time is very nice: thank you! :)
I can run your example LDpair(var1 = "rs3", var2 = "rs4", pop = "YRI", token = Sys.getenv("LDLINK_TOKEN"))
without any problem, but I have been having some issue when using pairs of SNPs that are not in LD.
library(LDlinkR)
my_var1 <- "rs2860773"
my_var2 <- "rs2631669"
Using output = text
, everything works:
LDpair(my_var1,
my_var2,
pop="EUR",
token=Sys.getenv("LDLINK_TOKEN"), output = "text")
# Query SNPs:
# rs2860773 (chr2:65665641)
# rs2631669 (chr2:66104881)
#
# EUR Haplotypes:
# rs2631669
# C T
# -----------------
# G | 326 | 273 | 599 (0.595)
# rs2860773 -----------------
# T | 210 | 197 | 407 (0.405)
# -----------------
# 536 470 1006
# (0.533) (0.467)
#
# G_C: 326 (0.324)
# G_T: 273 (0.271)
# T_C: 210 (0.209)
# T_T: 197 (0.196)
#
# D': 0.0316
# R2: 0.0008
# Chi-sq: 0.778
# p-value: 0.3777
#
# rs2860773 and rs2631669 are in linkage equilibrium
But using output = table
(default), I get this error message:
LDpair(my_var1,
my_var2,
pop="EUR",
token=Sys.getenv("LDLINK_TOKEN")
# Error in z[[22]] : subscript out of bounds
From what I understand, it comes from your function table_out()
that expects 22 lines as it is when variants are in LD (in your example):
21 : "rs3(C) allele is correlated with rs4(A) allele"
22 : "rs3(T) allele is correlated with rs4(G) allele"
But when variants are actually in linkage equilibrium, these two lines are replaced by a single one (my example):
21 : "rs2860773 and rs2631669 are in linkage equilibrium"
This should be quite easy to fix! ;)
Thanks again for this very useful package!
Prepare for release:
git pull
usethis::use_github_links()
urlchecker::url_check()
devtools::check(remote = TRUE, manual = TRUE)
devtools::check_win_devel()
revdepcheck::revdep_check()
cran-comments.md
git push
Submit to CRAN:
devtools::submit_cran()
Wait for CRAN...
usethis::use_github_release()
usethis::use_version("minor")
usethis::use_dev_version()
git push all master
Add function for citation of publication
Change from 3.5.2 to >= 3.4.2
Prepare for release:
git pull
urlchecker::url_check()
devtools::check(remote = TRUE, manual = TRUE)
devtools::check_win_devel()
rhub::check_for_cran()
revdepcheck::revdep_check(num_workers = 4)
cran-comments.md
git push
Submit to CRAN:
usethis::use_version('minor')
devtools::submit_cran()
Wait for CRAN...
git push
usethis::use_github_release()
usethis::use_dev_version()
git push
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