timyers / ldlinkr Goto Github PK

LDproxy_batch stops processing a list of SNPs when it encounters a variant that is not biallelic.

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Add function for citation of publication

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.

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!

Change from 3.5.2 to >= 3.4.2

Add PDF of extended examples as vignette

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.

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