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issue with FUSION.post_process.R --omnibus #58

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yangrousong opened this issue Jun 25, 2023 · 0 comments
Open

issue with FUSION.post_process.R --omnibus #58

yangrousong opened this issue Jun 25, 2023 · 0 comments

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@yangrousong
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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.
2. 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.

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