Merge branch 'main' of https://github.com/TiffanyAmariuta/TCSC into main

TiffanyAmariuta · Jun 9, 2023 · ea08529 · ea08529
2 parents 64d9958 + bda46e4
commit ea08529
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diff --git a/README.md b/README.md
@@ -32,8 +32,8 @@ git clone https://github.com/gusevlab/fusion_twas
 
 4. Download and unzip LD reference files for 1000 Genomes European population
 ```
-wget https://storage.googleapis.com/broad-alkesgroup-public/LDSCORE/1000G_Phase3_plinkfiles.tgz
-tar zxvf 1000G_Phase3_plinkfiles.tgz
+wget https://data.broadinstitute.org/alkesgroup/FUSION/LDREF.tar.bz2
+tar xjvf LDREF.tar.bz2
 ```
 
 5. Download and unzip TCSC gene expression weight files
@@ -70,7 +70,7 @@ for tissue in `cat TissuesA.txt`
 do
 for chr in {1..22}
 do
-Rscript fusion_twas-master/FUSION.assoc_test.R --sumstats $your_genomewide_sumstats --weights TCSC/weights/320EUR_metatissues/${tissue}.pos --weights_dir TCSC_weight_files/weights/v8_320EUR --ref_ld_chr 1000G_EUR_Phase3_plink/1000G.EUR.QC. --chr $chr --out results_320/v8_320EUR.${trait}/v8_320EUR.${trait}.${tissue}.${chr}.dat
+Rscript fusion_twas-master/FUSION.assoc_test.R --sumstats $your_genomewide_sumstats --weights TCSC/weights/320EUR_metatissues/${tissue}.pos --weights_dir TCSC_weight_files/weights/v8_320EUR --ref_ld_chr LDREF/1000G.EUR. --chr $chr --out results_320/v8_320EUR.${trait}/v8_320EUR.${trait}.${tissue}.${chr}.dat
 done
 done
 
@@ -79,7 +79,7 @@ for tissue in `cat TissuesB.txt`
 do
 for chr in {1..22}
 do
-Rscript fusion_twas-master/FUSION.assoc_test.R --sumstats $your_genomewide_sumstats --weights TCSC/weights/allEUR_tissues/v8_allEUR_${tissue}_blup.pos --weights_dir TCSC_weight_files/weights --ref_ld_chr 1000G_EUR_Phase3_plink/1000G.EUR.QC. --chr $chr --out results_all/v8_allEUR.${trait}/v8_allEUR.${trait}.${tissue}.${chr}.dat
+Rscript fusion_twas-master/FUSION.assoc_test.R --sumstats $your_genomewide_sumstats --weights TCSC/weights/allEUR_tissues/v8_allEUR_${tissue}_blup.pos --weights_dir TCSC_weight_files/weights --ref_ld_chr LDREF/1000G.EUR. --chr $chr --out results_all/v8_allEUR.${trait}/v8_allEUR.${trait}.${tissue}.${chr}.dat
 done
 done
 
@@ -88,7 +88,7 @@ for tissue in `cat TissuesC.txt`
 do
 for chr in {1..22}
 do
-Rscript TCSC/analysis/FUSION.assoc_test.meta.R --sumstats $your_genomewide_sumstats --weights TCSC/weights/320EUR_metatissues/${tissue}.pos --weights_dir TCSC_weight_files/weights/v8_320EUR --ref_ld_chr 1000G_EUR_Phase3_plink/1000G.EUR.QC. --chr $chr --out results_320/v8_320EUR.${trait}/v8_320EUR.${trait}.${tissue}.${chr}.dat
+Rscript TCSC/analysis/FUSION.assoc_test.meta.R --sumstats $your_genomewide_sumstats --weights TCSC/weights/320EUR_metatissues/${tissue}.pos --weights_dir TCSC_weight_files/weights/v8_320EUR --ref_ld_chr LDREF/1000G.EUR. --chr $chr --out results_320/v8_320EUR.${trait}/v8_320EUR.${trait}.${tissue}.${chr}.dat
 done
 done
 ```

diff --git a/analysis/Run_TCSC.R b/analysis/Run_TCSC.R
@@ -37,9 +37,9 @@ transcript_key <- fread(paste0("TCSC/weights/heritablegenes/Nall/TranscriptsIn",
 keep <- fread(paste0("TCSC/weights/heritablegenes/Nall/TranscriptsIn",tissues[i],"Model_keep.txt"), header = F)$V1
 z <- fread(paste0("TCSC/twas_statistics/allEUR_GTEx/",trait,"/Marginal_alphas_",trait,"_",tissues[i],".txt.gz"), header = F)$V1
 }else{
-transcript_key <- fread(paste0("weights/heritablegenes/N320/TranscriptsIn",tissues[i],"Model.txt"), header = F)$V1
-keep <- fread(paste0("weights/heritablegenes/N320/TranscriptsIn",tissues[i],"Model_keep.txt"), header = F)$V1 
-z <- fread(paste0("twas_statistics/320EUR_GTEx/",trait,"/Marginal_alphas_",trait,"_",tissues[i],".txt.gz"), header = F)$V1
+transcript_key <- fread(paste0("TCSC/weights/heritablegenes/N320/TranscriptsIn",tissues[i],"Model.txt"), header = F)$V1
+keep <- fread(paste0("TCSC/weights/heritablegenes/N320/TranscriptsIn",tissues[i],"Model_keep.txt"), header = F)$V1 
+z <- fread(paste0("TCSC/twas_statistics/320EUR_GTEx/",trait,"/Marginal_alphas_",trait,"_",tissues[i],".txt.gz"), header = F)$V1
 }
 w <- which(transcript_key %in% keep)
 transcript_key <- transcript_key[w]