Each Tumor Type separated!!
folderNames <- c("BLCA_PRS_20211011",
"BRCA_PRS_20211011",
"CESC_PRS_20211011",
"CHOL_PRS_20211011",
"ESCA_PRS_20211011",
"GBM_PRS_20211011",
"HNSC_PRS_20211011",
"KICH_PRS_20211011",
"KIRC_PRS_20211011",
"KIRP_PRS_20211011",
"LIHC_PRS_20211011",
"LUAD_PRS_20211011",
"LUSC_PRS_20211011",
"PAAD_PRS_20211011",
"PRAD_PRS_20211011",
"SARC_PRS_20211011",
"SKCM_PRS_20211011",
"TGCT_PRS_20211011",
"UCEC_PRS_20211011",
"UCS_PRS_20211011"
)
for (i in 1:length(folderNames)){
#dir(file.path(getwd(),folderNames[i]), pattern = "20211011", full.names=F)
#df <- data.frame(gene=c(), trait=c(), p_value=c())
final<-data.frame()
tumorName <- folderNames[i]
fileNames <- dir(file.path(getwd(),folderNames[i]),pattern = "res.txt", full.names = F) #This will create a vector that contains the list of file names ending with "res.txt".
for (j in 1:length(fileNames)){
traitName<- fileNames[j]
print(traitName)
data <- read.table(file.path(getwd(),tumorName,traitName), comment="", header = TRUE)
#write.table(data, file = paste(traitName,".txt",sep=""), sep = "\t", quote = FALSE)
demodf<-data.frame(c(1),c(1))
for (k in 1:nrow(data)){
if (is.na(data[k,1])){
data[k,1] <- 1
}
if(is.na(data[k,2])){
data[k,1] <- 1
}
if (data[k,1] > data[k,2]){
demodf[k,] <- c(row.names(data[k,]),data[k,2])
} else{ demodf[k,] <- c(row.names(data[k,]), data[k,1])}
}
demodf<-demodf[order(demodf[,2]),]
demodf<- demodf[1:20,]
c<- rep(traitName,20)
df<-data.frame( gene =demodf[,1], trait = c, pval = demodf[,2])
final<- rbind(final, df)
}
final<-final[order(final[,1]),]
colnames(final)<- c("gene", "trait", "p_value")
write.table(final, file = paste(tumorName, "top20pval.txt", sep=""), sep = "\t", quote = FALSE, row.names=FALSE)
data <- read.table( paste(tumorName, "top20pval.txt", sep=""), comment="", header = TRUE)
data<- data[order(data$p_value),]
data<- data[1:20,]
write.table(data, file = paste(tumorName, "top20pval.txt", sep=""), sep = "\t", quote = FALSE, row.names=FALSE)
}## [1] NA## Warning in file(file, "rt"): cannot open file '/Users/jihyun/Desktop/PRS_histo/
## top20/BLCA_PRS_20211011/NA': No such file or directory## Error in file(file, "rt"): cannot open the connectionCheck the files that I created above.
fileNames <- dir(file.path(getwd()),pattern = "pval.txt", full.names = F)
for (i in 1:length(fileNames)){
data <- read.table(fileNames[i], comment="", header = TRUE)
print(i)
print(fileNames[i])
print(data)
}## [1] 1
## [1] "BLCA_PRS_20211011top20pval.txt"
## gene trait p_value
## 1 FTH1 Vitiligo_res.txt 0.0002769139
## 2 RNF111 T2D_DIAGRAM_2017_res.txt 0.0003455066
## 3 TP53 SmokingCessation_res.txt 0.0007401188
## 4 TRAF3IP2 PD_GWAS_2017_N300k_res.txt 0.0007739485
## 5 RNF111 ukbEUR_DIA2_res.txt 0.0008347651
## 6 CREBBP UC_NG_2015_res.txt 0.0008594374
## 7 CREBBP SCZ_Cell_2018_res.txt 0.0010783204
## 8 FMN2 Vitiligo_res.txt 0.0011396484
## 9 HIST1H1E DrinksPerWeek_res.txt 0.0011632889
## 10 ACTB Prostate_cancer_2017_common_res.txt 0.0013771109
## 11 PTEN EA_NG_2018_excluding_23andMe_res.txt 0.0014878141
## 12 SF1 ukbEUR_TI_cojo_res.txt 0.0019107998
## 13 PHF3 T2D_DIAGRAM_2017_res.txt 0.0021262579
## 14 ACTB Vitiligo_res.txt 0.0023826722
## 15 PIK3CA ukbEUR_PVD_res.txt 0.0024078293
## 16 MKI67 SmokingCessation_res.txt 0.0026282406
## 17 KIAA1522 PD_GWAS_2017_N300k_res.txt 0.0028537287
## 18 PIK3CA IQ_NG_2018_res.txt 0.0028632984
## 19 PIK3CA IQ_NG_2018.1_res.txt 0.0028632984
## 20 RNF111 ukbEUR_HEMORRHOIDS_res.txt 0.0028709435
## [1] 2
## [1] "BRCA_PRS_20211011top20pval.txt"
## gene trait p_value
## 1 TP53 SmokingCessation_res.txt 0.0007401188
## 2 CBFB T2D_DIAGRAM_2017_res.txt 0.0010473054
## 3 PTEN EA_NG_2018_excluding_23andMe_res.txt 0.0014878141
## 4 CDH1 ukbEUR_OSTIOP_res.txt 0.0018216125
## 5 PIK3CA ukbEUR_PVD_res.txt 0.0024078293
## 6 PIK3CA IQ_NG_2018_res.txt 0.0028632984
## 7 PIK3CA IQ_NG_2018.1_res.txt 0.0028632984
## 8 TP53 EA_NG_2018_excluding_23andMe_res.txt 0.0034598303
## 9 PTEN ukbEUR_OSTIOP_res.txt 0.0034648313
## 10 MAP2K4 ukbEUR_CANCER_res.txt 0.0037016650
## 11 FOXA1 DrinksPerWeek_res.txt 0.0053961927
## 12 MUC17 ukbEUR_DYSLIPID_res.txt 0.0055750835
## 13 SF3B1 ukbEUR_HYPER_res.txt 0.0068509853
## 14 RUNX1 PD_GWAS_2017_N300k_res.txt 0.0075980048
## 15 FBXW7 RA_NG2010.hap3_res.txt 0.0083137975
## 16 FBXW7 ukbEUR_DIA2_res.txt 0.0083876929
## 17 FBXW7 ukbEUR_CI_cojo_res.txt 0.0100089845
## 18 TP53 Prostate_cancer_2017_common_res.txt 0.0100880635
## 19 PTEN ukbEUR_CANCER_res.txt 0.0115651547
## 20 MAP3K1 UC_NG_2015_res.txt 0.0133613821
## [1] 3
## [1] "CESC_PRS_20211011top20pval.txt"
## gene trait p_value
## 1 ABCA12 T2D_DIAGRAM_2017_res.txt 0.0002164297
## 2 TP53 SmokingCessation_res.txt 0.0007401188
## 3 FLG ukbEUR_Height_res.txt 0.0007812806
## 4 PTEN EA_NG_2018_excluding_23andMe_res.txt 0.0014878141
## 5 FLG ukbEUR_CARD_res.txt 0.0023720818
## 6 PIK3CA ukbEUR_PVD_res.txt 0.0024078293
## 7 PIK3CA IQ_NG_2018_res.txt 0.0028632984
## 8 PIK3CA IQ_NG_2018.1_res.txt 0.0028632984
## 9 TP53 EA_NG_2018_excluding_23andMe_res.txt 0.0034598303
## 10 PTEN ukbEUR_OSTIOP_res.txt 0.0034648313
## 11 BAP1 ukbEUR_PSYCHIATRIC_res.txt 0.0034998197
## 12 FLG ukbEUR_ASTHMA_res.txt 0.0069526651
## 13 MAPK1 Prostate_cancer_2017_common_res.txt 0.0075311878
## 14 FBXW7 RA_NG2010.hap3_res.txt 0.0083137975
## 15 FBXW7 ukbEUR_DIA2_res.txt 0.0083876929
## 16 FLG Vitiligo_res.txt 0.0091563574
## 17 CASP8 CigarettesPerDay_res.txt 0.0092958334
## 18 CASP8 ukbEUR_DYSLIPID_res.txt 0.0099648285
## 19 FBXW7 ukbEUR_CI_cojo_res.txt 0.0100089845
## 20 TP53 Prostate_cancer_2017_common_res.txt 0.0100880635
## [1] 4
## [1] "CHOL_PRS_20211011top20pval.txt"
## gene trait p_value
## 1 DNAH5 Vitiligo_res.txt 0.0004671867
## 2 DNAH5 RA_NG2010.hap3_res.txt 0.0020602637
## 3 BAP1 ukbEUR_PSYCHIATRIC_res.txt 0.0034998197
## 4 DNAH5 SCZ_Cell_2018_res.txt 0.0047871641
## 5 ATG16L1 SCZ_Cell_2018_res.txt 0.0075287986
## 6 PBRM1 IQ_NG_2018_res.txt 0.0124424884
## 7 PBRM1 IQ_NG_2018.1_res.txt 0.0124424884
## 8 DNAH5 ukbEUR_PVD_res.txt 0.0139269786
## 9 BAP1 ukbEUR_PVD_res.txt 0.0171746991
## 10 PBRM1 Vitiligo_res.txt 0.0190849627
## 11 ATG16L1 ukbEUR_PVD_res.txt 0.0235689577
## 12 BAP1 ukbEUR_DIA2_res.txt 0.0291117006
## 13 BAP1 ukbEUR_OBESITY_res.txt 0.0297163470
## 14 DNAH5 T2D_DIAGRAM_2017_res.txt 0.0326469621
## 15 PBRM1 ukbEUR_CARD_res.txt 0.0330733089
## 16 PBRM1 RA_NG2010.hap3_res.txt 0.0335045213
## 17 DNAH5 ukbEUR_CANCER_res.txt 0.0403196180
## 18 ATG16L1 ukbEUR_OSTIOP_res.txt 0.0436618870
## 19 BAP1 ukbEUR_HEMORRHOIDS_res.txt 0.0480660320
## 20 ATG16L1 T2D_DIAGRAM_2017_res.txt 0.0539340733
## [1] 5
## [1] "ESCA_PRS_20211011top20pval.txt"
## gene trait p_value
## 1 TP53 SmokingCessation_res.txt 0.0007401188
## 2 PIK3CA ukbEUR_PVD_res.txt 0.0024078293
## 3 PIK3CA IQ_NG_2018_res.txt 0.0028632984
## 4 PIK3CA IQ_NG_2018.1_res.txt 0.0028632984
## 5 TP53 EA_NG_2018_excluding_23andMe_res.txt 0.0034598303
## 6 SMAD4 IQ_NG_2018_res.txt 0.0051795004
## 7 SMAD4 IQ_NG_2018.1_res.txt 0.0051795004
## 8 TP53 Prostate_cancer_2017_common_res.txt 0.0100880635
## 9 SLC17A6 ukbEUR_OSTIOA_res.txt 0.0117283395
## 10 SMARCA4 ukbEUR_HEMORRHOIDS_res.txt 0.0127122366
## 11 TP53 ukbEUR_CASES_res.txt 0.0176094196
## 12 SLC17A6 ukbEUR_CI_cojo_res.txt 0.0198172523
## 13 NAA16 IBD_NG2017.hap3_res.txt 0.0213335650
## 14 TP53 IQ_NG_2018_res.txt 0.0214374008
## 15 TP53 IQ_NG_2018.1_res.txt 0.0214374008
## 16 PIK3CA EA_NG_2018_excluding_23andMe_res.txt 0.0230011023
## 17 NFE2L2 ukbEUR_DIA2_res.txt 0.0232001439
## 18 SLC17A6 ukbEUR_OBESITY_res.txt 0.0233680500
## 19 NAA16 UC_NG_2015_res.txt 0.0309229050
## 20 SMAD4 ukbEUR_DYSLIPID_res.txt 0.0320156095
## [1] 6
## [1] "GBM_PRS_20211011top20pval.txt"
## gene trait p_value
## 1 EGFR EA_NG_2018_excluding_23andMe_res.txt 0.0004740343
## 2 LZTR1 ukbEUR_PSYCHIATRIC_res.txt 0.0005327073
## 3 EGFR IQ_NG_2018_res.txt 0.0006591103
## 4 EGFR IQ_NG_2018.1_res.txt 0.0006591103
## 5 TP53 SmokingCessation_res.txt 0.0007401188
## 6 PTEN EA_NG_2018_excluding_23andMe_res.txt 0.0014878141
## 7 LZTR1 PD_GWAS_2017_N300k_res.txt 0.0021066294
## 8 PIK3CA ukbEUR_PVD_res.txt 0.0024078293
## 9 PIK3CA IQ_NG_2018_res.txt 0.0028632984
## 10 PIK3CA IQ_NG_2018.1_res.txt 0.0028632984
## 11 TP53 EA_NG_2018_excluding_23andMe_res.txt 0.0034598303
## 12 PTEN ukbEUR_OSTIOP_res.txt 0.0034648313
## 13 GABRA6 SCZ_Cell_2018_res.txt 0.0044397037
## 14 LZTR1 T2D_DIAGRAM_2017_res.txt 0.0060306718
## 15 IL18RAP MDD_NG_2018_res.txt 0.0069643579
## 16 PIK3R1 ukbEUR_TI_cojo_res.txt 0.0090167500
## 17 LUM ukbEUR_Height_res.txt 0.0091905028
## 18 PIK3R1 SCZ_Cell_2018_res.txt 0.0100184373
## 19 TP53 Prostate_cancer_2017_common_res.txt 0.0100880635
## 20 RPL5 ukbEUR_DYSLIPID_res.txt 0.0105361097
## [1] 7
## [1] "HNSC_PRS_20211011top20pval.txt"
## gene trait p_value
## 1 HLA-A ukbEUR_CI_cojo_res.txt 0.0002212435
## 2 TP53 SmokingCessation_res.txt 0.0007401188
## 3 NSD1 ukbEUR_PVD_res.txt 0.0011092138
## 4 THSD7A CigarettesPerDay_res.txt 0.0012157936
## 5 PTEN EA_NG_2018_excluding_23andMe_res.txt 0.0014878141
## 6 KEAP1 PD_GWAS_2017_N300k_res.txt 0.0021675894
## 7 GPATCH8 ukbEUR_OSTIOP_res.txt 0.0023927649
## 8 PIK3CA ukbEUR_PVD_res.txt 0.0024078293
## 9 GPATCH8 RA_NG2010.hap3_res.txt 0.0026242661
## 10 HLA-A ukbEUR_BMI_res.txt 0.0028476582
## 11 PIK3CA IQ_NG_2018_res.txt 0.0028632984
## 12 PIK3CA IQ_NG_2018.1_res.txt 0.0028632984
## 13 TP53 EA_NG_2018_excluding_23andMe_res.txt 0.0034598303
## 14 PTEN ukbEUR_OSTIOP_res.txt 0.0034648313
## 15 NSD1 ukbEUR_PEPTIC_ULCERS_res.txt 0.0048931031
## 16 RARG IQ_NG_2018_res.txt 0.0051681766
## 17 RARG IQ_NG_2018.1_res.txt 0.0051681766
## 18 SMAD4 IQ_NG_2018_res.txt 0.0051795004
## 19 SMAD4 IQ_NG_2018.1_res.txt 0.0051795004
## 20 NSD1 CigarettesPerDay_res.txt 0.0066747184
## [1] 8
## [1] "KICH_PRS_20211011top20pval.txt"
## gene trait p_value
## 1 TP53 SmokingCessation_res.txt 0.0007401188
## 2 FRG1 ukbEUR_DYSLIPID_res.txt 0.0033358421
## 3 TP53 EA_NG_2018_excluding_23andMe_res.txt 0.0034598303
## 4 TP53 Prostate_cancer_2017_common_res.txt 0.0100880635
## 5 TP53 ukbEUR_CASES_res.txt 0.0176094196
## 6 TP53 IQ_NG_2018_res.txt 0.0214374008
## 7 TP53 IQ_NG_2018.1_res.txt 0.0214374008
## 8 FRG1 ukbEUR_CARD_res.txt 0.0293939313
## 9 TP53 ukbEUR_TI_cojo_res.txt 0.0389900734
## 10 TP53 ukbEUR_OSTIOA_res.txt 0.0595673904
## 11 FRG1 SmokingCessation_res.txt 0.0623154913
## 12 TP53 CigarettesPerDay_res.txt 0.0673896380
## 13 TP53 SWB_NG_2015_res.txt 0.0791582883
## 14 FRG1 ukbEUR_CI_cojo_res.txt 0.1150304458
## 15 TP53 MDD_NG_2018_res.txt 0.1160794638
## 16 FRG1 IBD_NG2017.hap3_res.txt 0.1346881465
## 17 TP53 ukbEUR_Height_res.txt 0.1394949103
## 18 FRG1 ukbEUR_VARICOSE_VEINS_res.txt 0.1690146090
## 19 TP53 DrinksPerWeek_res.txt 0.1963375151
## 20 FRG1 SWB_NG_2015_res.txt 0.1972382558
## [1] 9
## [1] "KIRC_PRS_20211011top20pval.txt"
## gene trait p_value
## 1 NOS1 ukbEUR_OBESITY_res.txt 0.0006276049
## 2 TP53 SmokingCessation_res.txt 0.0007401188
## 3 PTEN EA_NG_2018_excluding_23andMe_res.txt 0.0014878141
## 4 VHL ukbEUR_OBESITY_res.txt 0.0023679925
## 5 TP53 EA_NG_2018_excluding_23andMe_res.txt 0.0034598303
## 6 PTEN ukbEUR_OSTIOP_res.txt 0.0034648313
## 7 BAP1 ukbEUR_PSYCHIATRIC_res.txt 0.0034998197
## 8 VHL RA_NG2010.hap3_res.txt 0.0058610353
## 9 VHL ukbEUR_BMI_res.txt 0.0070159046
## 10 TP53 Prostate_cancer_2017_common_res.txt 0.0100880635
## 11 PTEN ukbEUR_CANCER_res.txt 0.0115651547
## 12 SETD2 Vitiligo_res.txt 0.0123358166
## 13 PBRM1 IQ_NG_2018_res.txt 0.0124424884
## 14 PBRM1 IQ_NG_2018.1_res.txt 0.0124424884
## 15 NOS1 Vitiligo_res.txt 0.0146257972
## 16 BAP1 ukbEUR_PVD_res.txt 0.0171746991
## 17 TP53 ukbEUR_CASES_res.txt 0.0176094196
## 18 NOS1 ukbEUR_OSTIOA_res.txt 0.0185103733
## 19 PBRM1 Vitiligo_res.txt 0.0190849627
## 20 ATM ukbEUR_ASTHMA_res.txt 0.0191745135
## [1] 10
## [1] "KIRP_PRS_20211011top20pval.txt"
## gene trait p_value
## 1 SMARCA4 ukbEUR_HEMORRHOIDS_res.txt 0.01271224
## 2 CUL3 Prostate_cancer_2017_common_res.txt 0.01342059
## 3 CUL3 ukbEUR_HERNIA_ABDOMINOPELVIC_res.txt 0.01936885
## 4 MET SmokingCessation_res.txt 0.02628956
## 5 MET EA_NG_2018_excluding_23andMe_res.txt 0.03599149
## 6 KRAS ukbEUR_CARD_res.txt 0.04568369
## 7 MET ukbEUR_ASTHMA_res.txt 0.04607232
## 8 SMARCA4 Prostate_cancer_2017_common_res.txt 0.04847619
## 9 SMARCA4 ukbEUR_PVD_res.txt 0.04948129
## 10 MET ukbEUR_Height_res.txt 0.06689932
## 11 MET IQ_NG_2018_res.txt 0.06713455
## 12 MET IQ_NG_2018.1_res.txt 0.06713455
## 13 CUL3 ukbEUR_PVD_res.txt 0.07415749
## 14 MET ukbEUR_ALLERGIC_RHINITIS_res.txt 0.08035187
## 15 MET ukbEUR_CI_cojo_res.txt 0.09090835
## 16 SMARCA4 ukbEUR_HYPER_res.txt 0.09879460
## 17 SMARCA4 CigarettesPerDay_res.txt 0.09991760
## 18 MET T2D_DIAGRAM_2017_res.txt 0.10295348
## 19 MET PD_GWAS_2017_N300k_res.txt 0.10401327
## 20 MET ukbEUR_BMI_res.txt 0.11077365
## [1] 11
## [1] "LIHC_PRS_20211011top20pval.txt"
## gene trait p_value
## 1 TP53 SmokingCessation_res.txt 0.0007401188
## 2 KEAP1 PD_GWAS_2017_N300k_res.txt 0.0021675894
## 3 PCDHB16 ukbEUR_CANCER_res.txt 0.0021761148
## 4 TP53 EA_NG_2018_excluding_23andMe_res.txt 0.0034598303
## 5 BAP1 ukbEUR_PSYCHIATRIC_res.txt 0.0034998197
## 6 COL11A1 EA_NG_2018_excluding_23andMe_res.txt 0.0050359535
## 7 ARID2 Vitiligo_res.txt 0.0062926817
## 8 HNF1A ukbEUR_CASES_res.txt 0.0077910223
## 9 CTNNB1 Vitiligo_res.txt 0.0089100472
## 10 COL11A1 SmokingCessation_res.txt 0.0095347877
## 11 TP53 Prostate_cancer_2017_common_res.txt 0.0100880635
## 12 AXIN1 ukbEUR_IRON_DEFICIENCY_res.txt 0.0110449047
## 13 HNF1A ukbEUR_CARD_res.txt 0.0123147715
## 14 RB1 IBD_NG2017.hap3_res.txt 0.0143402527
## 15 BAP1 ukbEUR_PVD_res.txt 0.0171746991
## 16 TP53 ukbEUR_CASES_res.txt 0.0176094196
## 17 HNF1A RA_NG2010.hap3_res.txt 0.0192544089
## 18 PCDHB16 Vitiligo_res.txt 0.0201713061
## 19 TP53 IQ_NG_2018_res.txt 0.0214374008
## 20 TP53 IQ_NG_2018.1_res.txt 0.0214374008
## [1] 12
## [1] "LUAD_PRS_20211011top20pval.txt"
## gene trait p_value
## 1 EGFR EA_NG_2018_excluding_23andMe_res.txt 0.0004740343
## 2 EGFR IQ_NG_2018_res.txt 0.0006591103
## 3 EGFR IQ_NG_2018.1_res.txt 0.0006591103
## 4 TP53 SmokingCessation_res.txt 0.0007401188
## 5 KEAP1 PD_GWAS_2017_N300k_res.txt 0.0021675894
## 6 TP53 EA_NG_2018_excluding_23andMe_res.txt 0.0034598303
## 7 BRAF Vitiligo_res.txt 0.0046410362
## 8 DZIP1L ukbEUR_HYPER_res.txt 0.0053861918
## 9 ARID2 Vitiligo_res.txt 0.0062926817
## 10 TP53 Prostate_cancer_2017_common_res.txt 0.0100880635
## 11 BRAF ukbEUR_OSTIOP_res.txt 0.0109926260
## 12 LCE1F ukbEUR_HEMORRHOIDS_res.txt 0.0117301686
## 13 SETD2 Vitiligo_res.txt 0.0123358166
## 14 SMARCA4 ukbEUR_HEMORRHOIDS_res.txt 0.0127122366
## 15 EGFR ukbEUR_DIA2_res.txt 0.0132844394
## 16 BRAF T2D_DIAGRAM_2017_res.txt 0.0134928488
## 17 DZIP1L ukbEUR_PSYCHIATRIC_res.txt 0.0139728711
## 18 KCNQ2 DrinksPerWeek_res.txt 0.0142328375
## 19 RB1 IBD_NG2017.hap3_res.txt 0.0143402527
## 20 DZIP1L ukbEUR_CASES_res.txt 0.0146838692
## [1] 13
## [1] "LUSC_PRS_20211011top20pval.txt"
## gene trait p_value
## 1 TP53 SmokingCessation_res.txt 0.0007401188
## 2 PTEN EA_NG_2018_excluding_23andMe_res.txt 0.0014878141
## 3 KEAP1 PD_GWAS_2017_N300k_res.txt 0.0021675894
## 4 PIK3CA ukbEUR_PVD_res.txt 0.0024078293
## 5 PIK3CA IQ_NG_2018_res.txt 0.0028632984
## 6 PIK3CA IQ_NG_2018.1_res.txt 0.0028632984
## 7 TP53 EA_NG_2018_excluding_23andMe_res.txt 0.0034598303
## 8 PTEN ukbEUR_OSTIOP_res.txt 0.0034648313
## 9 TP53 Prostate_cancer_2017_common_res.txt 0.0100880635
## 10 PTEN ukbEUR_CANCER_res.txt 0.0115651547
## 11 ADAMTS12 ukbEUR_CANCER_res.txt 0.0121119974
## 12 RB1 IBD_NG2017.hap3_res.txt 0.0143402527
## 13 ELTD1 IQ_NG_2018_res.txt 0.0166844865
## 14 ELTD1 IQ_NG_2018.1_res.txt 0.0166844865
## 15 TP53 ukbEUR_CASES_res.txt 0.0176094196
## 16 PTEN ukbEUR_DYSLIPID_res.txt 0.0209265850
## 17 TP53 IQ_NG_2018_res.txt 0.0214374008
## 18 TP53 IQ_NG_2018.1_res.txt 0.0214374008
## 19 DPPA4 ukbEUR_OSTIOA_res.txt 0.0223135875
## 20 ADAMTS12 SWB_NG_2015_res.txt 0.0225604157
## [1] 14
## [1] "PAAD_PRS_20211011top20pval.txt"
## gene trait p_value
## 1 TP53 SmokingCessation_res.txt 0.0007401188
## 2 RNF43 Vitiligo_res.txt 0.0022529261
## 3 TP53 EA_NG_2018_excluding_23andMe_res.txt 0.0034598303
## 4 SMAD4 IQ_NG_2018_res.txt 0.0051795004
## 5 SMAD4 IQ_NG_2018.1_res.txt 0.0051795004
## 6 RNF43 SmokingInitiation_res.txt 0.0054623390
## 7 RNF43 ukbEUR_HEMORRHOIDS_res.txt 0.0089476290
## 8 TP53 Prostate_cancer_2017_common_res.txt 0.0100880635
## 9 RNF43 ukbEUR_CASES_res.txt 0.0161825409
## 10 TP53 ukbEUR_CASES_res.txt 0.0176094196
## 11 RNF43 ukbEUR_PEPTIC_ULCERS_res.txt 0.0208808450
## 12 TP53 IQ_NG_2018_res.txt 0.0214374008
## 13 TP53 IQ_NG_2018.1_res.txt 0.0214374008
## 14 SMAD4 ukbEUR_DYSLIPID_res.txt 0.0320156095
## 15 COTL1 ukbEUR_Height_res.txt 0.0333056868
## 16 SMAD4 ukbEUR_CASES_res.txt 0.0348276787
## 17 ARID1A Vitiligo_res.txt 0.0386561376
## 18 TGFBR2 Prostate_cancer_2017_common_res.txt 0.0386676118
## 19 TP53 ukbEUR_TI_cojo_res.txt 0.0389900734
## 20 RNF43 ukbEUR_PVD_res.txt 0.0406247770
## [1] 15
## [1] "PRAD_PRS_20211011top20pval.txt"
## gene trait p_value
## 1 TP53 SmokingCessation_res.txt 0.0007401188
## 2 PTEN EA_NG_2018_excluding_23andMe_res.txt 0.0014878141
## 3 PIK3CA ukbEUR_PVD_res.txt 0.0024078293
## 4 PIK3CA IQ_NG_2018_res.txt 0.0028632984
## 5 PIK3CA IQ_NG_2018.1_res.txt 0.0028632984
## 6 TP53 EA_NG_2018_excluding_23andMe_res.txt 0.0034598303
## 7 PTEN ukbEUR_OSTIOP_res.txt 0.0034648313
## 8 ETV3 ukbEUR_CANCER_res.txt 0.0038410392
## 9 COL11A1 EA_NG_2018_excluding_23andMe_res.txt 0.0050359535
## 10 FOXA1 DrinksPerWeek_res.txt 0.0053961927
## 11 CSMD3 CigarettesPerDay_res.txt 0.0066818934
## 12 CSMD3 Vitiligo_res.txt 0.0082218430
## 13 CTNNB1 Vitiligo_res.txt 0.0089100472
## 14 APC SmokingCessation_res.txt 0.0091074202
## 15 COL11A1 SmokingCessation_res.txt 0.0095347877
## 16 CDK12 ukbEUR_Height_res.txt 0.0098727412
## 17 TP53 Prostate_cancer_2017_common_res.txt 0.0100880635
## 18 PTEN ukbEUR_CANCER_res.txt 0.0115651547
## 19 HRAS ukbEUR_ALLERGIC_RHINITIS_res.txt 0.0129706910
## 20 TP53 ukbEUR_CASES_res.txt 0.0176094196
## [1] 16
## [1] "SARC_PRS_20211011top20pval.txt"
## gene trait p_value
## 1 TP53 SmokingCessation_res.txt 0.0007401188
## 2 PTEN EA_NG_2018_excluding_23andMe_res.txt 0.0014878141
## 3 TP53 EA_NG_2018_excluding_23andMe_res.txt 0.0034598303
## 4 PTEN ukbEUR_OSTIOP_res.txt 0.0034648313
## 5 TP53 Prostate_cancer_2017_common_res.txt 0.0100880635
## 6 PTEN ukbEUR_CANCER_res.txt 0.0115651547
## 7 RB1 IBD_NG2017.hap3_res.txt 0.0143402527
## 8 TP53 ukbEUR_CASES_res.txt 0.0176094196
## 9 PTEN ukbEUR_DYSLIPID_res.txt 0.0209265850
## 10 TP53 IQ_NG_2018_res.txt 0.0214374008
## 11 TP53 IQ_NG_2018.1_res.txt 0.0214374008
## 12 TP53 ukbEUR_TI_cojo_res.txt 0.0389900734
## 13 PTEN ukbEUR_HYPER_res.txt 0.0561274529
## 14 TP53 ukbEUR_OSTIOA_res.txt 0.0595673904
## 15 PTEN IQ_NG_2018_res.txt 0.0631094823
## 16 PTEN IQ_NG_2018.1_res.txt 0.0631094823
## 17 TP53 CigarettesPerDay_res.txt 0.0673896380
## 18 PTEN ukbEUR_BMI_res.txt 0.0705249109
## 19 TP53 SWB_NG_2015_res.txt 0.0791582883
## 20 RB1 ukbEUR_ASTHMA_res.txt 0.0847995682
## [1] 17
## [1] "SKCM_PRS_20211011top20pval.txt"
## gene trait p_value
## 1 TP53 SmokingCessation_res.txt 0.0007401188
## 2 PTEN EA_NG_2018_excluding_23andMe_res.txt 0.0014878141
## 3 TP53 EA_NG_2018_excluding_23andMe_res.txt 0.0034598303
## 4 PTEN ukbEUR_OSTIOP_res.txt 0.0034648313
## 5 BRAF Vitiligo_res.txt 0.0046410362
## 6 TACR3 SWB_NG_2015_res.txt 0.0054176895
## 7 TACR3 ukbEUR_CARD_res.txt 0.0060376556
## 8 ARID2 Vitiligo_res.txt 0.0062926817
## 9 PPP6C IQ_NG_2018_res.txt 0.0068315121
## 10 PPP6C IQ_NG_2018.1_res.txt 0.0068315121
## 11 PCDHB8 ukbEUR_CANCER_res.txt 0.0068877067
## 12 RGS22 EA_NG_2018_excluding_23andMe_res.txt 0.0069086006
## 13 PDE1A Vitiligo_res.txt 0.0091564573
## 14 TP53 Prostate_cancer_2017_common_res.txt 0.0100880635
## 15 BRAF ukbEUR_OSTIOP_res.txt 0.0109926260
## 16 PTEN ukbEUR_CANCER_res.txt 0.0115651547
## 17 HNF4G DrinksPerWeek_res.txt 0.0119596151
## 18 PDE1A ukbEUR_HERNIA_ABDOMINOPELVIC_res.txt 0.0119630749
## 19 TACR3 ukbEUR_CI_cojo_res.txt 0.0132622991
## 20 MAP2K1 Vitiligo_res.txt 0.0133605335
## [1] 18
## [1] "TGCT_PRS_20211011top20pval.txt"
## gene trait p_value
## 1 NRAS Vitiligo_res.txt 0.01471168
## 2 NRAS ukbEUR_CANCER_res.txt 0.01890556
## 3 NRAS PD_GWAS_2017_N300k_res.txt 0.02760321
## 4 NRAS UC_NG_2015_res.txt 0.03117181
## 5 KIT ukbEUR_HYPER_res.txt 0.03510323
## 6 NRAS ukbEUR_CARD_res.txt 0.04059930
## 7 KRAS ukbEUR_CARD_res.txt 0.04568369
## 8 NRAS ukbEUR_CI_cojo_res.txt 0.04648172
## 9 NRAS SCZ_Cell_2018_res.txt 0.05467952
## 10 KIT RA_NG2010.hap3_res.txt 0.05963490
## 11 NRAS RA_NG2010.hap3_res.txt 0.07749342
## 12 NRAS IBD_NG2017.hap3_res.txt 0.08849419
## 13 KIT DrinksPerWeek_res.txt 0.09761553
## 14 KIT ukbEUR_CANCER_res.txt 0.10379842
## 15 NRAS ukbEUR_ALLERGIC_RHINITIS_res.txt 0.10654215
## 16 NRAS ukbEUR_BMI_res.txt 0.10813569
## 17 KRAS Prostate_cancer_2017_common_res.txt 0.13788269
## 18 KRAS ukbEUR_CI_cojo_res.txt 0.13851455
## 19 KRAS ukbEUR_HERNIA_ABDOMINOPELVIC_res.txt 0.14602245
## 20 KRAS SmokingCessation_res.txt 0.15801640
## [1] 19
## [1] "UCEC_PRS_20211011top20pval.txt"
## gene trait p_value
## 1 LZTR1 ukbEUR_PSYCHIATRIC_res.txt 0.0005327073
## 2 TP53 SmokingCessation_res.txt 0.0007401188
## 3 PTEN EA_NG_2018_excluding_23andMe_res.txt 0.0014878141
## 4 RAB3GAP1 ukbEUR_OSTIOA_res.txt 0.0020103956
## 5 LZTR1 PD_GWAS_2017_N300k_res.txt 0.0021066294
## 6 PIK3CA ukbEUR_PVD_res.txt 0.0024078293
## 7 PIK3CA IQ_NG_2018_res.txt 0.0028632984
## 8 PIK3CA IQ_NG_2018.1_res.txt 0.0028632984
## 9 TP53 EA_NG_2018_excluding_23andMe_res.txt 0.0034598303
## 10 PTEN ukbEUR_OSTIOP_res.txt 0.0034648313
## 11 SIN3A SWB_NG_2015_res.txt 0.0046834651
## 12 DEPDC1B CigarettesPerDay_res.txt 0.0053695489
## 13 LZTR1 T2D_DIAGRAM_2017_res.txt 0.0060306718
## 14 CCND1 DrinksPerWeek_res.txt 0.0074740545
## 15 DICER1 ukbEUR_CI_cojo_res.txt 0.0078437661
## 16 FBXW7 RA_NG2010.hap3_res.txt 0.0083137975
## 17 FBXW7 ukbEUR_DIA2_res.txt 0.0083876929
## 18 CTNNB1 Vitiligo_res.txt 0.0089100472
## 19 PIK3R1 ukbEUR_TI_cojo_res.txt 0.0090167500
## 20 DEPDC1B ukbEUR_TI_cojo_res.txt 0.0091919665
## [1] 20
## [1] "UCS_PRS_20211011top20pval.txt"
## gene trait p_value
## 1 TP53 SmokingCessation_res.txt 0.0007401188
## 2 PTEN EA_NG_2018_excluding_23andMe_res.txt 0.0014878141
## 3 PIK3CA ukbEUR_PVD_res.txt 0.0024078293
## 4 PIK3CA IQ_NG_2018_res.txt 0.0028632984
## 5 PIK3CA IQ_NG_2018.1_res.txt 0.0028632984
## 6 FOXA2 IQ_NG_2018_res.txt 0.0031145590
## 7 FOXA2 IQ_NG_2018.1_res.txt 0.0031145590
## 8 TP53 EA_NG_2018_excluding_23andMe_res.txt 0.0034598303
## 9 PTEN ukbEUR_OSTIOP_res.txt 0.0034648313
## 10 FBXW7 RA_NG2010.hap3_res.txt 0.0083137975
## 11 ERBB3 ukbEUR_VARICOSE_VEINS_res.txt 0.0083334877
## 12 FBXW7 ukbEUR_DIA2_res.txt 0.0083876929
## 13 FBXW7 ukbEUR_CI_cojo_res.txt 0.0100089845
## 14 TP53 Prostate_cancer_2017_common_res.txt 0.0100880635
## 15 PTEN ukbEUR_CANCER_res.txt 0.0115651547
## 16 FBXW7 ukbEUR_VARICOSE_VEINS_res.txt 0.0140152547
## 17 RB1 IBD_NG2017.hap3_res.txt 0.0143402527
## 18 CHD4 ukbEUR_DIA2_res.txt 0.0144040172
## 19 TP53 ukbEUR_CASES_res.txt 0.0176094196
## 20 ZBTB7B RA_NG2010.hap3_res.txt 0.0201046007