First, thanks @sashagusev for developing and maintaining this tool.I just got into the TWAS field， so i have many issue. 1. When i combine the two files into on one file and run FUSION.post_process.R --omnibus, I found that there are no graphs in the generated results. The code I ran is as follows: Rscript $PathSoftware/FUSION.post_process.R --omnibus \
--sumstats $PathSummary/SFC${PhenoName}.txt \
--input $OutPath/SFC${PhenoName}.${Chr}.top \
--out $OutPath_PostAnalysis/SFC${PhenoName}.${Chr}.top.analysis \
--ref_ld_chr $PathSoftware/LDREF/1000G.EUR. \
--chr $Chr \
--plot \
--locus_win 100000.
When I Test for effect in CMC.BRAIN.RNASEQ_SPLICING (ZNF561) and TCGA-GBM.TUMOR.ZNF846_162993.wgt.RDat TCGA-SARC.TUMOR.ZNF846_162993.wgt.RDat TCGA-HNSC.TUMOR.ZNF846_162993.wgt.RDat TCGA-LGG.TUMOR.ZNF561_93134.wgt.RDat TCGA-LGG.TUMOR.ZNF846_162993.wgt.RDat. The result (.CORR.dat) only appeared CMC.BRAIN.RNASEQ_SPLICING (ZNF561) and TCGA-LGG.TUMOR.ZNF561_93134.wgt.RDat as follow:
GENE REF1 REF2 CORR
ZNF561 CMC.BRAIN.RNASEQ_SPLICING TCGA-LGG.TUMOR -0.701
I don't know how to understand this part of the content, perhaps you can tell me where to go to seek a solution.
First, thanks @sashagusev for developing and maintaining this tool.I just got into the TWAS field， so i have many issue. 1. When i combine the two files into on one file and run FUSION.post_process.R --omnibus, I found that there are no graphs in the generated results. The code I ran is as follows: Rscript $PathSoftware/FUSION.post_process.R --omnibus \ --sumstats $PathSummary/SFC${PhenoName}.txt \ --input $OutPath/SFC${PhenoName}.${Chr}.top \ --out $OutPath_PostAnalysis/SFC${PhenoName}.${Chr}.top.analysis \ --ref_ld_chr $PathSoftware/LDREF/1000G.EUR. \ --chr $Chr \ --plot \ --locus_win 100000.