search

gusevlab / fusion_twas

methods for functional summary-based imputation
http://gusevlab.org/projects/fusion/
GNU General Public License v3.0
75 stars 45 forks source link

No *.RDat output generate for compute weights script #22

Closed Bochao1 closed 4 years ago

Bochao1 commented 4 years ago

Dear all,

I am a new user for FUSION. I want compute weights using my own expressional dataset, and I am try to repeat the example script. There is only .hsq files (no .RDat) generated after I run the commend line 59.
https://github.com/gusevlab/fusion_twas/blob/ef9c47546c6c9aa1386f32ab633da9188fa28587/examples/GEUV.compute_weights.sh#L59

However, the manual mentioned "Assuming $TMP, $INP, and $OUT are defined, this will take as input the $INP.bed/bim/fam file and generate a $OUT.RDat file which contains the expression weights and performance statistics for this gene."

In addition, I did not figure out how to generate $TMP file in the script.

Is any important steps were missing? The software version are below (tested all software work well) GEMMA: 0.98.1 PLINK: 1.90 gcta: https://github.com/gusevlab/fusion_twas/blob/master/gcta_nr_robust

Thank you very much!

Best, Bochao Lin

sashagusev commented 4 years ago

Hi Bochao, have you filled in the paths in lines 4,5,6,9,21 and all those directories exist?