Hi,
I’m trying to run a multivariate GWAS using GenomicSEM. I munged the sumstats, did ldsc and I’m having error with the function sumstats, see below:
files ← c(“ftnd_wave3_meta_analysis_summary_stats.all_chr.eur.txt”,“…/…/sumstats/originals/GSCAN_SmkInit_2022_GWAS_SUMMARY_STATS_EUR_modifiedRenata.txt”,“…/…/sumstats/originals/GSCAN_SmkCes_2022_GWAS_SUMMARY_STATS_EUR_modifiedRenata.txt”,“…/…/sumstats/originals/GSCAN_CigDay_2022_GWAS_SUMMARY_STATS_EUR_modifiedRenata.txt”,“TUD_meta_eur_maf_withoutUKBB_JM_MVJ_0817231_checked.txt”)
N ← c(46213, 783474, 280295, 326497, 606283)
trait.names ← c(“FTND”, “SmkInit”, “SmkCes”, “CPD”, “TUD”)
se.logit ← c(F,F,F,F,F)
linprob ← c(T,T,T,F,T)
OLS ← c(F,F,F,T,F)
ref ← “reference.1000G.maf.0.005.txt.gz”
betas ← c(“Effect”,“BETA”,“BETA”, “BETA”,“Zscore”)
smoking_multivar ←
sumstats(files=files,ref=ref,trait.names=trait.names,se.logit=se.logit,OLS = OLS,linprob=linprob,N=N,betas=betas, info.filter=.6, maf.filter=0.01,keep.indel=FALSE,parallel=TRUE,cores=NULL)
smoking_multivar ← sumstats(files=files,ref=ref,trait.names=trait.names,se.logit=se.logit,OLS = OLS,linprob=linprob,N=N,betas=betas, info.filter=.6, maf.filter=0.01,keep.indel=FALSE,parallel=TRUE,cores=NULL)
The preparation of 5 summary statistics for use in Genomic SEM began at: 2024-08-15 14:34:37
Please note that the files should be in the same order that they were listed for the ldsc function
Reading in reference file
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Applying MAF filer of 0.01 to the reference file.
Number of requested cores(79) greater than the number of files (5). Deferring to the lowest number
As parallel sumstats was requested, logs of each file will be saved separately
Error in { :
task 1 failed - “operations are possible only for numeric, logical or complex types”
I tryed to exclude the sumstats file 1 each time and check them to see any non-numerical value and didn’t find any problem.
Any idea what could be the problem?
Thank you!
Renata