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mglev1n / locusplotr

Create Regional Association Plots
https://mglev1n.github.io/locusplotr
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Error in `ld_extract_locuszoom()`: ! Reference variant is missing from the specified LD panel when running "ld_extract_locuszoom" function #4

Closed amingjie228 closed 6 months ago

amingjie228 commented 6 months ago

When I run "ld_extract_locuszoom" function, I encounter this error. However, the example data can provide the corresponding results.

ld_extract_locuszoom(chrom = 10, pos = 46044649, ref = "G", alt = "A", start = 46033307 - 5e4, stop = 46048180 + 5e4, genome_build = "GRCh38", population = "ALL", metric = "rsquare") ℹ Extracting LD for 10:46044649_G/A for the region 10:45983307-46098180 ℹ Initial query failed - trying again with flipped Ref/Alt Error in ld_extract_locuszoom(): ! Reference variant is missing from the specified LD panel

and this is my data:

head(MSMB) chromosome position rsid effect_allele other_allele eaf effect std_err p_value 1: 10 45983346 rs71257889 C G 0.41760 -0.0238 0.008481 5.014e-03 2: 10 45983869 rs71277324 A G 0.26269 -0.1199 0.009453 7.279e-37 3: 10 45983944 rs61849500 A G 0.00399 0.3462 0.064763 9.010e-08 4: 10 45983949 rs1411783984 T G 0.00355 0.2657 0.068827 1.132e-04 5: 10 45984066 rs1325250454 T G 0.01791 -0.1826 0.030796 3.040e-09 6: 10 45984211 rs1213672813 C T 0.00037 0.4462 0.224149 4.652e-02

mglev1n commented 6 months ago

The variant that you're trying to query (10:46044649:G:A) doesn't exist in the reference panel. If you look up that variant in gnomAD, it doesn't seem to exist in either GRCh38 (or GRCh37): https://gnomad.broadinstitute.org/variant/10-46044649-G-A. The function queries the University of Michigan LocusZoom API, which serves information from the 1000 Genomes reference panels: https://portaldev.sph.umich.edu/docs/api/v1/#introduction