Open KirakiraZLY opened 2 months ago
Hello @KirakiraZLY , thank you for submitting an issue!
I first used the full script from your page, but I had some problems with the Loading LD reference and with running calculateLD.R. So I copied the part about calculating the LD matrix from Florian's page (The part on Correlation) and got the error above.
About calculateLD.R, I got the error saying --file-ld-blocks is not a defined optional argument or flag
.
This is my configuration:
export fileOutLD=ld-chr-@.rds
export fileOutLDMap=ld-map.rds
Rscript ${software_dir}/calculateLD.R --geno-file-rds $fileGenoRDS \
--dir-genetic-maps interpolated_from_hapmap \
--sumstats $fileSumstats Predictor \
--file-ld-blocks $fileOutLD \
--file-ld-map $fileOutLDMap
Hi,
Thanks very much for making this script of LDpred2. However, I got the following error, which I didn't see before. Do you have any idea about what was going on?
I believe this happened when it ran through this code:
ind.row <- rows_along(G)
Do I need to change the bound limit or reduce the size of my genotype file? And 1047164 < 1047164 this sentence makes no idea to me.
😊