Hello,
I am trying to run this program FUSION.assoc_test.R from :
http://gusevlab.org/projects/fusion/#typical-analysis-and-output
[t.cri.asokovic@cri16in002 fusion_twas-master]$ Rscript FUSION.assoc_test.R
\
> --sumstats /gpfs/data/stranger-lab/anamaria/meta_gwas/META_CHR22_1.txt \
> --weights ./weight/retina.pos \
> --weights_dir ./weight/ \
> --ref_ld_chr ./LDREF/1000G.EUR.22 \
> --chr 22 \
> --out PGC2.SCZ.22.dat
Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
Calls: load -> readChar
In addition: Warning message:
In readChar(con, 5L, useBytes = TRUE) :
cannot open compressed file './weight//NA', probable reason 'No such file
or directory'
Execution halted
I also formatted my retina.pos to be the same as in the given example (the
example does run for me)
WGT ID CHR P0 P1
retina/retina.ENSG00000000419.wgt.RDat DPM1 chr20 50934867
50958555
retina/retina.ENSG00000000457.wgt.RDat SCYL3 chr1 169849631
169894267
retina/retina.ENSG00000000460.wgt.RDat C1orf112 chr1 169662007
169854080
retina/retina.ENSG00000000938.wgt.RDat FGR chr1 27612064
27635277
retina/retina.ENSG00000000971.wgt.RDat CFH chr1 196651878
196747504
[t.cri.asokovic@cri16in002 weight]$ ls
retina retina.pos
[t.cri.asokovic@cri16in002 weight]$ pwd
/gpfs/data/stranger-lab/anamaria/fusion/fusion_twas-master/weight
in retina folder I have all .RDat files
Does anyone know what is the issue here? It is impossible to get an answer
from the developer.
Thanks
Ana
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