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error in vctrs #18

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Cui4399 opened this issue Feb 24, 2024 · 1 comment
Open

error in vctrs #18

Cui4399 opened this issue Feb 24, 2024 · 1 comment

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@Cui4399
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Cui4399 commented Feb 24, 2024

My exposure and outcome data are both from Finngen, log files for ldsc and munge seems normal,and my codes are as follows:
reslap = MRlap(exposure = GP,

  •            exposure_name = "GP",
    
  •            outcome = SD,
    
  •            outcome_name = "SD",
    
  •            ld = "/home/ubuntu/ldsc/eur_w_ld_chr/",
    
  •            hm3 = "/home/ubuntu/MRLAP/filesNeed/w_hm3.snplist",
    
  •            MR_threshold = 5e-10,
    
  •            MR_pruning_LD = 0.05,
    
  •            save_logfiles=TRUE)
    

<<< Preparation of analysis >>>

Checking parameters
The p-value threshold used for selecting MR instruments is: 5e-10
The distance used for pruning MR instruments is: 500 Kb
The LD threshold used for pruning MR instruments is: 0.05
Processing exposure (GP) summary statistics...

Preparation of the data...

The data.frame used as input is: "GP".
SNPID column, ok - CHR column, ok - POS column, ok - ALT column, ok - REF column, ok - BETA column, ok - SE column, ok - N column, ok

Processing outcome (SD) summary statistics...

Preparation of the data...

The data.frame used as input is: "SD".
SNPID column, ok - CHR column, ok - POS column, ok - ALT column, ok - REF column, ok - BETA column, ok - SE column, ok - N column, ok
<><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
<<< Performing cross-trait LDSC >>>

Munging exposure data...
Please check the log file GP_munge.log to ensure that all columns were interpreted correctly and no warnings were issued for any of the summary statistics files
Munging outcome data...
Please check the log file SD_munge.log to ensure that all columns were interpreted correctly and no warnings were issued for any of the summary statistics files
Running cross-trait LDSC...
Please check the log file GP.sumstats.gz_SD.sumstats.gz_ldsc.log for detailed results of the cross-trait LDSC analysis
Cleaning temporary files...
<><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
<<< Running IVW-MR >>>
Error in vctrs::vec_locate_matches():
! Match procedure results in an allocation larger than 2^31-1 elements.
ℹ Attempted allocation size was 94013060093.
ℹ This is an internal error that was detected in the vctrs package.
Please report it at https://github.com/r-lib/vctrs/issues with a reprex (https://tidyverse.org/help/) and the full backtrace.
Run rlang::last_trace() to see where the error occurred.

@gabumon0
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to remove row when rsid=='' in outcome/exposure, maybe solve the problem

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