Recently I always encounter an error above while running bGWAS v1.0.2. I have used this version previously but this error never occurred; however, when I re-run the same analysis without any modification, the same error still occurred. Have you recently updated the package?
I tried to investigate the issue but was unsuccessful. Will you be able to fix this issue?
Many thanks,
patrick
1) Here is the script for the analysis:
B <- bGWAS(Z_matrices = file_directory,
name = output_name,
GWAS = MyGWAS,
prior_studies = NULL,
MR_threshold = 1e-6,
MR_ninstruments = 3,
MR_pruning_dist = 500,
MR_pruning_LD = 0,
MR_shrinkage = 1,
stepwise_threshold = NULL,
prior_shrinkage = NULL,
sign_method = "p",
sign_thresh = 1e-6,
use_permutations= FALSE,
res_pruning_dist = 500,
res_pruning_LD = 0,
save_files = TRUE,
verbose = TRUE)
2) and here are the log output:
<<< Preparation of analysis >>>
Checking parameters
The name of your analysis is: "bGWAS_allEC_26traits_1e-6".
The Z-Matrix files are stored in "C:\Users\xueminW\Desktop\allEC_bGWAS_26traits_exclude_RAFFH".
Preparation of the data...
The conventional GWAS used as input is:ecac_mr_file_noUKBB_cleaned.txt.gz (ID = 1).
The analysis will be run in the folder: "C:/Users/xueminW/Desktop/allEC_bGWAS_26traits_exclude_RAFFH".
Files will be saved in: "C:/Users/xueminW/Desktop/allEC_bGWAS_26traits_exclude_RAFFH/bGWAS_allEC_26traits_1e-6".
The study ecac_mr_file_noUKBB_cleaned.txt.gz (ID=1) has been removed from the prior GWASs used to build the prior since it is used as conventionnal GWAS.
The p-value threshold used for selecting MR instruments is: 1e-06.
The minimum number instruments required for each trait is: 3.
The distance used for pruning MR instruments is: 500Kb.
Distance-based pruning will be used for MR instruments.
No shrinkage applied before performing MR.The p-value threshold used for stepwise selection will be derived according to the number of Prior GWASs used.
Using MR_shrinkage as default for prior_shrinkage:No shrinkage applied before performing calculating the prior.The p-value threshold used for stepwise selection will be derived according to the number of Prior GWASs used.
Significant SNPs will be identified according to p-value. The threshold used is :1e-06.
The distance used for pruning results is: 500Kb.
Distance-based pruning will be used for results.
Initializing the summary information file
List of files : C:/Users/xueminW/Desktop/allEC_bGWAS_26traits_exclude_RAFFH/bGWAS_allEC_26traits_1e-6/PriorGWASs.csv has been successfully created.
<><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
<<< Identification of significant prior GWASs for MR >>>
Creating the Z-Matrix of strong instruments
Loading the ZMatrix...
Selecting studies :
25 studies
260,208 SNPs
Adding data from the conventional GWAS :
"ecac_mr_file_noUKBB_cleaned.txt.gz"
Done!
260,208 SNPs in common between prior studies and the conventional GWAS
Thresholding...
177,573 SNPs left after thresholding
25 studies left after thresholding
Pruning MR instruments...
distance : 500Kb
1,478 SNPs left after pruning
Oestradiol : removed (less than 3 strong instrument after pruning)
24 studies left after thresholding+pruning
1,477 SNPs left after removing studies with only one strong instrument
Error in file(file, ifelse(append, "a", "w")) :
cannot open the connection
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
cannot open file 'PriorGWASs.tsv': Invalid argument
Dear Ninon,
Recently I always encounter an error above while running bGWAS v1.0.2. I have used this version previously but this error never occurred; however, when I re-run the same analysis without any modification, the same error still occurred. Have you recently updated the package?
I tried to investigate the issue but was unsuccessful. Will you be able to fix this issue?
Many thanks, patrick
1) Here is the script for the analysis: B <- bGWAS(Z_matrices = file_directory, name = output_name, GWAS = MyGWAS, prior_studies = NULL, MR_threshold = 1e-6, MR_ninstruments = 3, MR_pruning_dist = 500, MR_pruning_LD = 0, MR_shrinkage = 1, stepwise_threshold = NULL, prior_shrinkage = NULL, sign_method = "p", sign_thresh = 1e-6, use_permutations= FALSE, res_pruning_dist = 500, res_pruning_LD = 0, save_files = TRUE, verbose = TRUE)
2) and here are the log output:
<<< Preparation of analysis >>>