Symlink genotype files into this directory. Set shell variable GENSCOT to the mountpoint of the HPC system holding copies of the data for compute:
ln -s ${GENSCOT}/genetics/genotypes/GS20K_PLINK_files/QCd_data/QCdGS20K.* .
ln -s ${GENSCOT}/genetics/imputed/HRC/updated_bims/GS20K_HRC_0.8_GCTA_*.* .
ln -s ${GENSCOT}/genetics/imputed/HRC/GS20K_HRC.INFO.gz .
Combine age/sex covariates with MDS components
library(readr)
library(dplyr)##
## Attaching package: 'dplyr'## The following objects are masked from 'package:stats':
##
## filter, lag## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, unionlibrary(stringr)
covars <- read_table2('plinkcovar.txt')## Parsed with column specification:
## cols(
## famid = col_double(),
## id = col_double(),
## age = col_double(),
## age2 = col_double(),
## sex = col_double()
## )pcs <- read_csv('HM3mds2R.mds.csv')## Parsed with column specification:
## cols(
## FID = col_double(),
## IID = col_double(),
## SOL = col_double(),
## C1 = col_double(),
## C2 = col_double(),
## C3 = col_double(),
## C4 = col_double()
## )## Warning: 988 parsing failures.
## row col expected actual file
## 19995 FID a double CEU 'HM3mds2R.mds.csv'
## 19996 FID a double CEU 'HM3mds2R.mds.csv'
## 19997 FID a double CEU 'HM3mds2R.mds.csv'
## 19998 FID a double CEU 'HM3mds2R.mds.csv'
## 19999 FID a double CEU 'HM3mds2R.mds.csv'
## ..... ... ........ ...... ..................
## See problems(...) for more details.all_covars <- pcs %>%
inner_join(covars, by=c('FID'='famid', 'IID'='id')) %>%
select(-SOL)
write_delim(all_covars, 'GenScot_AgeSexPCs.cov', delim=' ')Check sample size with all inclusions and exclusions applied
plink \
--bfile QCdGS20K \
--pheno QCdGS20K_Pheno_dep_status_Unaff_b_only0_Aff_b_only1.txt \
--keep QCdGS20K_unrelated_t0.025.fam \
--remove GSindividualsOverlappingWithUKB500K.txt \
--freq case-control \
--maf 0.01 \
--out GenScot_MDD_rmUKBB \
--memory 3000
plink \
--bfile QCdGS20K \
--pheno QCdGS20K_Pheno_dep_status_Unaff_b_only0_Aff_b_only1.txt \
--covar GenScot_AgeSexPCs.cov \
--keep QCdGS20K_unrelated_t0.025.fam \
--remove GSindividualsOverlappingWithUKB500K.txt \
--maf 0.01 \
--logistic \
--ci 0.95 \
--out Genscot_MDD_rmUKBB \
--memory 3000
GSrmUKBB.frq.sh:
#$ -N GSrmUKBB.frq
#$ -l h_rt=1:00:00
#$ -l h_vmem=4G
#$ -t 1-22
#$ -cwd
#$ -e logs
#$ -o logs
. /etc/profile.d/modules.sh
module load igmm/apps/plink/1.90b4
CHR=$SGE_TASK_ID
plink \
--bfile GS20K_HRC_0.8_GCTA_${CHR} \
--pheno QCdGS20K_Pheno_dep_status_Unaff_b_only0_Aff_b_only1.txt \
--keep QCdGS20K_unrelated_t0.025.fam \
--remove GSindividualsOverlappingWithUKB500K.txt \
--freq case-control \
--out GenScot_MDD_rmUKBB.HRC.${CHR} \
--memory 3000
qsub GSrmUKBB.frq.sh
GSrmUKBB.assoc.sh:
#$ -N GSrmUKBB.assoc
#$ -l h_rt=1:00:00
#$ -l h_vmem=4G
#$ -t 1-22
#$ -cwd
#$ -e logs
#$ -o logs
. /etc/profile.d/modules.sh
module load igmm/apps/plink/1.90b4
CHR=$SGE_TASK_ID
plink \
--bfile GS20K_HRC_0.8_GCTA_${CHR} \
--pheno QCdGS20K_Pheno_dep_status_Unaff_b_only0_Aff_b_only1.txt \
--covar GenScot_AgeSexPCs.cov \
--keep QCdGS20K_unrelated_t0.025.fam \
--remove GSindividualsOverlappingWithUKB500K.txt \
--logistic \
--ci 0.95 \
--maf 0.01 \
--out GenScot_MDD_rmUKBB.HRC.${CHR} \
--memory 3000
qsub GSrmUKBB.assoc.sh
Open frequency and association results files. Convert to daner format
freq <- bind_rows(plyr::llply(1:22, function(chr) read_table2(paste0('GenScot_MDD_rmUKBB.HRC.', chr, '.frq.cc'))))## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## A1 = col_character(),
## A2 = col_character(),
## MAF_A = col_double(),
## MAF_U = col_double(),
## NCHROBS_A = col_double(),
## NCHROBS_U = col_double()
## )
## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## A1 = col_character(),
## A2 = col_character(),
## MAF_A = col_double(),
## MAF_U = col_double(),
## NCHROBS_A = col_double(),
## NCHROBS_U = col_double()
## )
## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## A1 = col_character(),
## A2 = col_character(),
## MAF_A = col_double(),
## MAF_U = col_double(),
## NCHROBS_A = col_double(),
## NCHROBS_U = col_double()
## )
## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## A1 = col_character(),
## A2 = col_character(),
## MAF_A = col_double(),
## MAF_U = col_double(),
## NCHROBS_A = col_double(),
## NCHROBS_U = col_double()
## )
## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## A1 = col_character(),
## A2 = col_character(),
## MAF_A = col_double(),
## MAF_U = col_double(),
## NCHROBS_A = col_double(),
## NCHROBS_U = col_double()
## )
## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## A1 = col_character(),
## A2 = col_character(),
## MAF_A = col_double(),
## MAF_U = col_double(),
## NCHROBS_A = col_double(),
## NCHROBS_U = col_double()
## )
## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## A1 = col_character(),
## A2 = col_character(),
## MAF_A = col_double(),
## MAF_U = col_double(),
## NCHROBS_A = col_double(),
## NCHROBS_U = col_double()
## )
## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## A1 = col_character(),
## A2 = col_character(),
## MAF_A = col_double(),
## MAF_U = col_double(),
## NCHROBS_A = col_double(),
## NCHROBS_U = col_double()
## )
## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## A1 = col_character(),
## A2 = col_character(),
## MAF_A = col_double(),
## MAF_U = col_double(),
## NCHROBS_A = col_double(),
## NCHROBS_U = col_double()
## )
## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## A1 = col_character(),
## A2 = col_character(),
## MAF_A = col_double(),
## MAF_U = col_double(),
## NCHROBS_A = col_double(),
## NCHROBS_U = col_double()
## )
## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## A1 = col_character(),
## A2 = col_character(),
## MAF_A = col_double(),
## MAF_U = col_double(),
## NCHROBS_A = col_double(),
## NCHROBS_U = col_double()
## )
## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## A1 = col_character(),
## A2 = col_character(),
## MAF_A = col_double(),
## MAF_U = col_double(),
## NCHROBS_A = col_double(),
## NCHROBS_U = col_double()
## )
## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## A1 = col_character(),
## A2 = col_character(),
## MAF_A = col_double(),
## MAF_U = col_double(),
## NCHROBS_A = col_double(),
## NCHROBS_U = col_double()
## )
## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## A1 = col_character(),
## A2 = col_character(),
## MAF_A = col_double(),
## MAF_U = col_double(),
## NCHROBS_A = col_double(),
## NCHROBS_U = col_double()
## )
## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## A1 = col_character(),
## A2 = col_character(),
## MAF_A = col_double(),
## MAF_U = col_double(),
## NCHROBS_A = col_double(),
## NCHROBS_U = col_double()
## )
## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## A1 = col_character(),
## A2 = col_character(),
## MAF_A = col_double(),
## MAF_U = col_double(),
## NCHROBS_A = col_double(),
## NCHROBS_U = col_double()
## )
## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## A1 = col_character(),
## A2 = col_character(),
## MAF_A = col_double(),
## MAF_U = col_double(),
## NCHROBS_A = col_double(),
## NCHROBS_U = col_double()
## )
## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## A1 = col_character(),
## A2 = col_character(),
## MAF_A = col_double(),
## MAF_U = col_double(),
## NCHROBS_A = col_double(),
## NCHROBS_U = col_double()
## )
## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## A1 = col_character(),
## A2 = col_character(),
## MAF_A = col_double(),
## MAF_U = col_double(),
## NCHROBS_A = col_double(),
## NCHROBS_U = col_double()
## )
## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## A1 = col_character(),
## A2 = col_character(),
## MAF_A = col_double(),
## MAF_U = col_double(),
## NCHROBS_A = col_double(),
## NCHROBS_U = col_double()
## )
## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## A1 = col_character(),
## A2 = col_character(),
## MAF_A = col_double(),
## MAF_U = col_double(),
## NCHROBS_A = col_double(),
## NCHROBS_U = col_double()
## )
## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## A1 = col_character(),
## A2 = col_character(),
## MAF_A = col_double(),
## MAF_U = col_double(),
## NCHROBS_A = col_double(),
## NCHROBS_U = col_double()
## )assoc <- bind_rows(plyr::llply(1:22, function(chr) read_table2(paste0('GenScot_MDD_rmUKBB.HRC.', chr, '.assoc.logistic'))))## Warning: Missing column names filled in: 'X13' [13]## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## BP = col_double(),
## A1 = col_character(),
## TEST = col_character(),
## NMISS = col_double(),
## OR = col_double(),
## SE = col_double(),
## L95 = col_double(),
## U95 = col_double(),
## STAT = col_double(),
## P = col_double(),
## X13 = col_character()
## )## Warning: 4539520 parsing failures.
## row col expected actual file
## 1 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.1.assoc.logistic'
## 2 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.1.assoc.logistic'
## 3 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.1.assoc.logistic'
## 4 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.1.assoc.logistic'
## 5 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.1.assoc.logistic'
## ... ... .......... .......... .........................................
## See problems(...) for more details.
## Warning: Missing column names filled in: 'X13' [13]## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## BP = col_double(),
## A1 = col_character(),
## TEST = col_character(),
## NMISS = col_double(),
## OR = col_double(),
## SE = col_double(),
## L95 = col_double(),
## U95 = col_double(),
## STAT = col_double(),
## P = col_double(),
## X13 = col_character()
## )## Warning: 4990368 parsing failures.
## row col expected actual file
## 1 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.2.assoc.logistic'
## 2 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.2.assoc.logistic'
## 3 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.2.assoc.logistic'
## 4 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.2.assoc.logistic'
## 5 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.2.assoc.logistic'
## ... ... .......... .......... .........................................
## See problems(...) for more details.
## Warning: Missing column names filled in: 'X13' [13]## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## BP = col_double(),
## A1 = col_character(),
## TEST = col_character(),
## NMISS = col_double(),
## OR = col_double(),
## SE = col_double(),
## L95 = col_double(),
## U95 = col_double(),
## STAT = col_double(),
## P = col_double(),
## X13 = col_character()
## )## Warning: 4250464 parsing failures.
## row col expected actual file
## 1 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.3.assoc.logistic'
## 2 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.3.assoc.logistic'
## 3 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.3.assoc.logistic'
## 4 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.3.assoc.logistic'
## 5 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.3.assoc.logistic'
## ... ... .......... .......... .........................................
## See problems(...) for more details.
## Warning: Missing column names filled in: 'X13' [13]## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## BP = col_double(),
## A1 = col_character(),
## TEST = col_character(),
## NMISS = col_double(),
## OR = col_double(),
## SE = col_double(),
## L95 = col_double(),
## U95 = col_double(),
## STAT = col_double(),
## P = col_double(),
## X13 = col_character()
## )## Warning: 4311264 parsing failures.
## row col expected actual file
## 1 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.4.assoc.logistic'
## 2 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.4.assoc.logistic'
## 3 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.4.assoc.logistic'
## 4 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.4.assoc.logistic'
## 5 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.4.assoc.logistic'
## ... ... .......... .......... .........................................
## See problems(...) for more details.
## Warning: Missing column names filled in: 'X13' [13]## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## BP = col_double(),
## A1 = col_character(),
## TEST = col_character(),
## NMISS = col_double(),
## OR = col_double(),
## SE = col_double(),
## L95 = col_double(),
## U95 = col_double(),
## STAT = col_double(),
## P = col_double(),
## X13 = col_character()
## )## Warning: 3873288 parsing failures.
## row col expected actual file
## 1 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.5.assoc.logistic'
## 2 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.5.assoc.logistic'
## 3 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.5.assoc.logistic'
## 4 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.5.assoc.logistic'
## 5 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.5.assoc.logistic'
## ... ... .......... .......... .........................................
## See problems(...) for more details.
## Warning: Missing column names filled in: 'X13' [13]## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## BP = col_double(),
## A1 = col_character(),
## TEST = col_character(),
## NMISS = col_double(),
## OR = col_double(),
## SE = col_double(),
## L95 = col_double(),
## U95 = col_double(),
## STAT = col_double(),
## P = col_double(),
## X13 = col_character()
## )## Warning: 3966368 parsing failures.
## row col expected actual file
## 1 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.6.assoc.logistic'
## 2 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.6.assoc.logistic'
## 3 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.6.assoc.logistic'
## 4 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.6.assoc.logistic'
## 5 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.6.assoc.logistic'
## ... ... .......... .......... .........................................
## See problems(...) for more details.
## Warning: Missing column names filled in: 'X13' [13]## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## BP = col_double(),
## A1 = col_character(),
## TEST = col_character(),
## NMISS = col_double(),
## OR = col_double(),
## SE = col_double(),
## L95 = col_double(),
## U95 = col_double(),
## STAT = col_double(),
## P = col_double(),
## X13 = col_character()
## )## Warning: 3481168 parsing failures.
## row col expected actual file
## 1 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.7.assoc.logistic'
## 2 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.7.assoc.logistic'
## 3 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.7.assoc.logistic'
## 4 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.7.assoc.logistic'
## 5 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.7.assoc.logistic'
## ... ... .......... .......... .........................................
## See problems(...) for more details.
## Warning: Missing column names filled in: 'X13' [13]## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## BP = col_double(),
## A1 = col_character(),
## TEST = col_character(),
## NMISS = col_double(),
## OR = col_double(),
## SE = col_double(),
## L95 = col_double(),
## U95 = col_double(),
## STAT = col_double(),
## P = col_double(),
## X13 = col_character()
## )## Warning: 3327224 parsing failures.
## row col expected actual file
## 1 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.8.assoc.logistic'
## 2 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.8.assoc.logistic'
## 3 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.8.assoc.logistic'
## 4 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.8.assoc.logistic'
## 5 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.8.assoc.logistic'
## ... ... .......... .......... .........................................
## See problems(...) for more details.
## Warning: Missing column names filled in: 'X13' [13]## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## BP = col_double(),
## A1 = col_character(),
## TEST = col_character(),
## NMISS = col_double(),
## OR = col_double(),
## SE = col_double(),
## L95 = col_double(),
## U95 = col_double(),
## STAT = col_double(),
## P = col_double(),
## X13 = col_character()
## )## Warning: 2551352 parsing failures.
## row col expected actual file
## 1 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.9.assoc.logistic'
## 2 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.9.assoc.logistic'
## 3 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.9.assoc.logistic'
## 4 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.9.assoc.logistic'
## 5 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.9.assoc.logistic'
## ... ... .......... .......... .........................................
## See problems(...) for more details.
## Warning: Missing column names filled in: 'X13' [13]## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## BP = col_double(),
## A1 = col_character(),
## TEST = col_character(),
## NMISS = col_double(),
## OR = col_double(),
## SE = col_double(),
## L95 = col_double(),
## U95 = col_double(),
## STAT = col_double(),
## P = col_double(),
## X13 = col_character()
## )## Warning: 3041280 parsing failures.
## row col expected actual file
## 1 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.10.assoc.logistic'
## 2 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.10.assoc.logistic'
## 3 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.10.assoc.logistic'
## 4 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.10.assoc.logistic'
## 5 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.10.assoc.logistic'
## ... ... .......... .......... ..........................................
## See problems(...) for more details.
## Warning: Missing column names filled in: 'X13' [13]## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## BP = col_double(),
## A1 = col_character(),
## TEST = col_character(),
## NMISS = col_double(),
## OR = col_double(),
## SE = col_double(),
## L95 = col_double(),
## U95 = col_double(),
## STAT = col_double(),
## P = col_double(),
## X13 = col_character()
## )## Warning: 2977224 parsing failures.
## row col expected actual file
## 1 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.11.assoc.logistic'
## 2 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.11.assoc.logistic'
## 3 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.11.assoc.logistic'
## 4 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.11.assoc.logistic'
## 5 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.11.assoc.logistic'
## ... ... .......... .......... ..........................................
## See problems(...) for more details.
## Warning: Missing column names filled in: 'X13' [13]## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## BP = col_double(),
## A1 = col_character(),
## TEST = col_character(),
## NMISS = col_double(),
## OR = col_double(),
## SE = col_double(),
## L95 = col_double(),
## U95 = col_double(),
## STAT = col_double(),
## P = col_double(),
## X13 = col_character()
## )## Warning: 2864504 parsing failures.
## row col expected actual file
## 1 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.12.assoc.logistic'
## 2 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.12.assoc.logistic'
## 3 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.12.assoc.logistic'
## 4 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.12.assoc.logistic'
## 5 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.12.assoc.logistic'
## ... ... .......... .......... ..........................................
## See problems(...) for more details.
## Warning: Missing column names filled in: 'X13' [13]## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## BP = col_double(),
## A1 = col_character(),
## TEST = col_character(),
## NMISS = col_double(),
## OR = col_double(),
## SE = col_double(),
## L95 = col_double(),
## U95 = col_double(),
## STAT = col_double(),
## P = col_double(),
## X13 = col_character()
## )## Warning: 2225272 parsing failures.
## row col expected actual file
## 1 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.13.assoc.logistic'
## 2 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.13.assoc.logistic'
## 3 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.13.assoc.logistic'
## 4 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.13.assoc.logistic'
## 5 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.13.assoc.logistic'
## ... ... .......... .......... ..........................................
## See problems(...) for more details.
## Warning: Missing column names filled in: 'X13' [13]## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## BP = col_double(),
## A1 = col_character(),
## TEST = col_character(),
## NMISS = col_double(),
## OR = col_double(),
## SE = col_double(),
## L95 = col_double(),
## U95 = col_double(),
## STAT = col_double(),
## P = col_double(),
## X13 = col_character()
## )## Warning: 1939184 parsing failures.
## row col expected actual file
## 1 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.14.assoc.logistic'
## 2 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.14.assoc.logistic'
## 3 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.14.assoc.logistic'
## 4 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.14.assoc.logistic'
## 5 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.14.assoc.logistic'
## ... ... .......... .......... ..........................................
## See problems(...) for more details.
## Warning: Missing column names filled in: 'X13' [13]## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## BP = col_double(),
## A1 = col_character(),
## TEST = col_character(),
## NMISS = col_double(),
## OR = col_double(),
## SE = col_double(),
## L95 = col_double(),
## U95 = col_double(),
## STAT = col_double(),
## P = col_double(),
## X13 = col_character()
## )## Warning: 1673680 parsing failures.
## row col expected actual file
## 1 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.15.assoc.logistic'
## 2 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.15.assoc.logistic'
## 3 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.15.assoc.logistic'
## 4 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.15.assoc.logistic'
## 5 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.15.assoc.logistic'
## ... ... .......... .......... ..........................................
## See problems(...) for more details.
## Warning: Missing column names filled in: 'X13' [13]## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## BP = col_double(),
## A1 = col_character(),
## TEST = col_character(),
## NMISS = col_double(),
## OR = col_double(),
## SE = col_double(),
## L95 = col_double(),
## U95 = col_double(),
## STAT = col_double(),
## P = col_double(),
## X13 = col_character()
## )## Warning: 1805392 parsing failures.
## row col expected actual file
## 1 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.16.assoc.logistic'
## 2 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.16.assoc.logistic'
## 3 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.16.assoc.logistic'
## 4 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.16.assoc.logistic'
## 5 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.16.assoc.logistic'
## ... ... .......... .......... ..........................................
## See problems(...) for more details.
## Warning: Missing column names filled in: 'X13' [13]## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## BP = col_double(),
## A1 = col_character(),
## TEST = col_character(),
## NMISS = col_double(),
## OR = col_double(),
## SE = col_double(),
## L95 = col_double(),
## U95 = col_double(),
## STAT = col_double(),
## P = col_double(),
## X13 = col_character()
## )## Warning: 1521432 parsing failures.
## row col expected actual file
## 1 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.17.assoc.logistic'
## 2 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.17.assoc.logistic'
## 3 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.17.assoc.logistic'
## 4 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.17.assoc.logistic'
## 5 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.17.assoc.logistic'
## ... ... .......... .......... ..........................................
## See problems(...) for more details.
## Warning: Missing column names filled in: 'X13' [13]## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## BP = col_double(),
## A1 = col_character(),
## TEST = col_character(),
## NMISS = col_double(),
## OR = col_double(),
## SE = col_double(),
## L95 = col_double(),
## U95 = col_double(),
## STAT = col_double(),
## P = col_double(),
## X13 = col_character()
## )## Warning: 1704280 parsing failures.
## row col expected actual file
## 1 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.18.assoc.logistic'
## 2 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.18.assoc.logistic'
## 3 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.18.assoc.logistic'
## 4 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.18.assoc.logistic'
## 5 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.18.assoc.logistic'
## ... ... .......... .......... ..........................................
## See problems(...) for more details.
## Warning: Missing column names filled in: 'X13' [13]## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## BP = col_double(),
## A1 = col_character(),
## TEST = col_character(),
## NMISS = col_double(),
## OR = col_double(),
## SE = col_double(),
## L95 = col_double(),
## U95 = col_double(),
## STAT = col_double(),
## P = col_double(),
## X13 = col_character()
## )## Warning: 1273352 parsing failures.
## row col expected actual file
## 1 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.19.assoc.logistic'
## 2 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.19.assoc.logistic'
## 3 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.19.assoc.logistic'
## 4 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.19.assoc.logistic'
## 5 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.19.assoc.logistic'
## ... ... .......... .......... ..........................................
## See problems(...) for more details.
## Warning: Missing column names filled in: 'X13' [13]## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## BP = col_double(),
## A1 = col_character(),
## TEST = col_character(),
## NMISS = col_double(),
## OR = col_double(),
## SE = col_double(),
## L95 = col_double(),
## U95 = col_double(),
## STAT = col_double(),
## P = col_double(),
## X13 = col_character()
## )## Warning: 1328880 parsing failures.
## row col expected actual file
## 1 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.20.assoc.logistic'
## 2 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.20.assoc.logistic'
## 3 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.20.assoc.logistic'
## 4 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.20.assoc.logistic'
## 5 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.20.assoc.logistic'
## ... ... .......... .......... ..........................................
## See problems(...) for more details.
## Warning: Missing column names filled in: 'X13' [13]## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## BP = col_double(),
## A1 = col_character(),
## TEST = col_character(),
## NMISS = col_double(),
## OR = col_double(),
## SE = col_double(),
## L95 = col_double(),
## U95 = col_double(),
## STAT = col_double(),
## P = col_double(),
## X13 = col_character()
## )## Warning: 812352 parsing failures.
## row col expected actual file
## 1 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.21.assoc.logistic'
## 2 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.21.assoc.logistic'
## 3 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.21.assoc.logistic'
## 4 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.21.assoc.logistic'
## 5 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.21.assoc.logistic'
## ... ... .......... .......... ..........................................
## See problems(...) for more details.
## Warning: Missing column names filled in: 'X13' [13]## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## BP = col_double(),
## A1 = col_character(),
## TEST = col_character(),
## NMISS = col_double(),
## OR = col_double(),
## SE = col_double(),
## L95 = col_double(),
## U95 = col_double(),
## STAT = col_double(),
## P = col_double(),
## X13 = col_character()
## )## Warning: 772776 parsing failures.
## row col expected actual file
## 1 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.22.assoc.logistic'
## 2 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.22.assoc.logistic'
## 3 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.22.assoc.logistic'
## 4 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.22.assoc.logistic'
## 5 -- 13 columns 12 columns 'GenScot_MDD_rmUKBB.HRC.22.assoc.logistic'
## ... ... .......... .......... ..........................................
## See problems(...) for more details.gs_bim <- read_table2('QCdGS20K.bim', col_names=c('CHR', 'SNP', 'CM', 'BP', 'A1', 'A2'))## Parsed with column specification:
## cols(
## CHR = col_double(),
## SNP = col_character(),
## CM = col_double(),
## BP = col_double(),
## A1 = col_character(),
## A2 = col_character()
## )hrc_info <- read_table2('GS20K_HRC.INFO.gz')## Parsed with column specification:
## cols(
## CHROM = col_double(),
## POS = col_double(),
## REF = col_character(),
## ALT = col_character(),
## INFO = col_double()
## )## Warning: 63 parsing failures.
## row col expected actual file
## 725028 CHROM a double CHROM 'GS20K_HRC.INFO.gz'
## 725028 POS a double POS 'GS20K_HRC.INFO.gz'
## 725028 INFO no trailing characters O 'GS20K_HRC.INFO.gz'
## 1426808 CHROM a double CHROM 'GS20K_HRC.INFO.gz'
## 1426808 POS a double POS 'GS20K_HRC.INFO.gz'
## ....... ..... ...................... ...... ...................
## See problems(...) for more details.# SNPs that are directly genotyped
genotyped <- gs_bim %>%
transmute(CHR, SNP, ngt=1)
sumstats <-
assoc %>%
filter(TEST == 'ADD') %>%
filter(str_detect(SNP, 'rs')) %>%
left_join(freq, by=c('CHR', 'SNP', 'A1')) %>%
left_join(genotyped, by=c('CHR', 'SNP')) %>%
left_join(hrc_info, by=c('CHR'='CHROM', 'BP'='POS')) %>%
mutate(ngt=if_else(ngt %in% 1, true=1, false=0)) %>%
select(CHR, SNP, BP, A1, A2, FRQ_A_951=MAF_A, FRQ_U_6114=MAF_U,
INFO, OR, SE, P, ngt) %>%
filter(!is.na(INFO) & FRQ_U_6114 >= 0.01 & FRQ_A_951 > 0.01)
write_tsv(sumstats, 'daner_mdd_genscot_2019-11a_rmUKBB.gz')