Questions about userGWAS:Error in crossprod(wls.diff, wls.v)

[Yifei L]

Hi,

I am using EFA for 16 traits to get 9 factors and I hoped to generate GWAS for factor6.

But I get the error below over and over again. 

Is there anyone can help? 

Thank you so much!!

Yifei

model<-"F1 =~ A + E + F + G + H

F2 =~ M + I + J + K + L

F3 =~ E + G +N + H

F4 =~ M + L + M + B + D

F5 =~ M + B +  A + E + G + H

F6 =~ M + C + E 

F7 =~ I + K + L + M

F8 =~ M + I + J

F9 =~ E + F 

F6 ~ SNP"

outputgwas<-userGWAS(covstruc = LDSCoutput_all, SNPs = all_sumstats, estimation = "DWLS", model = model, printwarn = FALSE, sub=c("F6 ~ SNP"), cores = NULL, toler = FALSE, SNPSE = FALSE, parallel =  FALSE  ,  GC="standard",MPI=FALSE,smooth_check=FALSE)

[1] "Please note that an update was made to userGWAS on 11/21/19 so that it combines addSNPs and userGWAS."

Error in crossprod(wls.diff, wls.v) : non-conformable arguments

[agro...@gmail.com]

Hi Yifei, 

Sorry for the late reply! You have a lot of variables that are loading on multiple factors, which may be causing some issues with convergence. Can you post the results you get when running the model using usermodel that does not include the effect of individual SNPs? 

Best, 

  Andrew