jennasimit / flashfm Goto Github PK

Dear Developer,
I have been trying to finemap causal variants for two related traits following the steps mentioned in ### SNP correlation matrix and RAF vector provided - run single-trait and multi-trait fine-mapping

The locus is represented by 4 SNPs that shows significant association in both the trait 1 and trait 2
Have compiled the following variables

snpinfo
covY
ybar (set to a vector of 0 for each of the trait)
beta
N
raf
corX (for the SNPs mentioned in the snpinfo and beta file)
Using rsIDs (and not as mentioned in the following note in the vignette)
NOTE: SNP names must not contain ":" in FLASHFMwithJAM, JAMexpanded.multi, and JAMexpandedCor.multi.
So, if SNP names are in the form "19:45301088_T_C" change to "chr19_45301088_T_C".

As I try to run the first step on single-trait mapping with the function FLASHFMwithJAM
The run goes through the iterations and crashes with the following error,
Error in dimnames(x) <- dn :
length of 'dimnames' [2] not equal to array extent

Debugging tells that the error takes place at the stage of the function JAMexpandedCor.multi

Is this known, any help or suggestions would be greatly appreciated.

Many thanks
M

Hi,

I'm trying the flashfm package, and there is a bug in FLASHFMwithFINEMAP function. The argument NCORES is not used in any function in FLASHFMwithFINEMAP, so it causes an error in flashfm.