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I am attempting to use local data for MVMR. I use the mv_extract_exposures_local function; package runs through all my traits and assesses LD structure. It runs through all the traits, but gives the error listed (see end of post) at the end of running through my traits and identifying which variants to keep/discard.
All required function components are in my dataset.
I have attempted running only lead SNPs for each locus and running datasets with all SNPs present (no LD restrictions). With both iterations, I get the same errors.
The last few lines of my console output (including the error) are below:
Clumping TNFRSF6B, 309 variants, using EUR population reference
Removing 308 of 309 variants due to LD with other variants or absence from LD reference panel
Identified 15 hits for trait CD160_log
Please look at vignettes for options on running this locally if you need to run many instances of this command.
Clumping 1, 15 variants, using EUR population reference
Removing 1 of 15 variants due to LD with other variants or absence from LD reference panel
Identified 14 variants to include
Error in mv_extract_exposures_local("/Users/T/sig_SNPs/All_withRSID_IDexposure.tsv", :
length(unique(d1$id)) == length(unique(id_exposure)) is not TRUE
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I am attempting to use local data for MVMR. I use the mv_extract_exposures_local function; package runs through all my traits and assesses LD structure. It runs through all the traits, but gives the error listed (see end of post) at the end of running through my traits and identifying which variants to keep/discard.
All required function components are in my dataset.
I have attempted running only lead SNPs for each locus and running datasets with all SNPs present (no LD restrictions). With both iterations, I get the same errors.
The last few lines of my console output (including the error) are below:
Clumping TNFRSF6B, 309 variants, using EUR population reference
Removing 308 of 309 variants due to LD with other variants or absence from LD reference panel
Identified 15 hits for trait CD160_log
Please look at vignettes for options on running this locally if you need to run many instances of this command.
Clumping 1, 15 variants, using EUR population reference
Removing 1 of 15 variants due to LD with other variants or absence from LD reference panel
Identified 14 variants to include
Error in mv_extract_exposures_local("/Users/T/sig_SNPs/All_withRSID_IDexposure.tsv", :
length(unique(d1$id)) == length(unique(id_exposure)) is not TRUE
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